ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data
Background Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent...
Saved in:
| Published in | BMC bioinformatics Vol. 21; no. 1; pp. 1 - 8 |
|---|---|
| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
BioMed Central
22.06.2020
BioMed Central Ltd Springer Nature B.V BMC |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1471-2105 1471-2105 |
| DOI | 10.1186/s12859-020-03585-4 |
Cover
| Abstract | Background
Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers.
Results
Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license.
Conclusions
ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at
https://github.com/metagenome-atlas/atlas
. |
|---|---|
| AbstractList | Background: Metagenomics and metatranscriptomics studies provide valuable insight into the composition and function of microbial populations from diverse environments, however the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. Results: Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome and metatranscriptome data. Genome-centric resolution and abundance estimates are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. Conclusions: ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome and metatranscriptome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas. Background Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. Results Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. Conclusions ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at Keywords: Metagenomics, Analysis workflow, Annotation, Metagenome-assembled genomes Background Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. Results Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. Conclusions ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas . Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers.BACKGROUNDMetagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers.Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license.RESULTSHere we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license.ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.CONCLUSIONSATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas. Abstract Background Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. Results Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. Conclusions ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas . Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas. Background Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. Results Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. Conclusions ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas. |
| ArticleNumber | 257 |
| Audience | Academic |
| Author | Zdobnov, Evgeny M. Brown, Joseph Kieser, Silas McCue, Lee Ann Trajkovski, Mirko |
| Author_xml | – sequence: 1 givenname: Silas surname: Kieser fullname: Kieser, Silas organization: Department of Cell Physiology and Metabolism, Faculty of Medicine, Centre Medical Universitaire, Swiss Institute of Bioinformatics – sequence: 2 givenname: Joseph surname: Brown fullname: Brown, Joseph organization: Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Current address: Department of Human Genetics, University of Utah – sequence: 3 givenname: Evgeny M. surname: Zdobnov fullname: Zdobnov, Evgeny M. organization: Swiss Institute of Bioinformatics, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Department of Genetic Medicine and Development, University of Geneva – sequence: 4 givenname: Mirko surname: Trajkovski fullname: Trajkovski, Mirko organization: Department of Cell Physiology and Metabolism, Faculty of Medicine, Centre Medical Universitaire, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Diabetes Center, Faculty of Medicine, Centre Medical Universitaire – sequence: 5 givenname: Lee Ann orcidid: 0000-0003-4456-517X surname: McCue fullname: McCue, Lee Ann email: leeann.mccue@pnnl.gov organization: Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory |
| BackLink | https://www.osti.gov/servlets/purl/1646625$$D View this record in Osti.gov |
| BookMark | eNqNkltv1DAQhSNURC_wB3iK4AUkUnyJnSwPSKuKS6VKSGx5tsbOJPU2sdvYy7L_Hu-momyFKhRFsSbfOfbM8XF24LzDLHtJySmltXwfKKvFrCCMFISLWhTlk-yIlhUtGCXi4K_1YXYcwpIQWtVEPMsOORMVZWR2lOH88mK--JBDvnBwjUN687Ufr9ver_PWjzmEgIPuN-9ycM5HiNa77brJO3R-sCbX1jnruty3-YARdmXMA96u0BnMG4jwPHvaQh_wxd33JPvx-dPl2dfi4tuX87P5RWEqSmOBpShR1Gh0pUWruWyE4RoYNprVvCS0JXwmBKS2mEgsB2QzEAQkbzXIGT_JziffxsNS3Yx2gHGjPFi1K_ixUzBGa3pUKDRwpmtWzXQpmKw1pZojaSU2pkKTvPjktXI3sFlD3_8xpERtA1BTACoFoHYBqDKpPk6qm5UekhO6OEK_d5T9P85eqc7_VBWnhKQuT7JXk4EP0apgbERzZbxzaKKispSSiQS9udtl9GnMIarBBoN9Dw79KihWUskkp3Lr9_oBuvSr0aUUEsV2k6zKe6qDNBvrWp8OZ7amai5ZJcqaM5ao039Q6WkwXYR0OVub6nuCt3uCxET8FTtYhaDOF9_32XpizehDGLFVqffddUub2P7xobMH0v9K6i7fkGDX4Xg_mEdUvwE4vhAM |
| CitedBy_id | crossref_primary_10_1016_j_isci_2024_110890 crossref_primary_10_1038_s41467_024_46033_0 crossref_primary_10_1128_msystems_01071_24 crossref_primary_10_1371_journal_pcbi_1009947 crossref_primary_10_1128_mra_01098_22 crossref_primary_10_3389_fmicb_2023_1072053 crossref_primary_10_3389_fnut_2022_1059163 crossref_primary_10_1093_ismeco_ycae076 crossref_primary_10_3389_fmicb_2023_1015666 crossref_primary_10_1016_j_dsr_2022_103744 crossref_primary_10_1016_j_cub_2025_01_068 crossref_primary_10_1038_s44220_023_00148_3 crossref_primary_10_1016_j_cmet_2020_08_012 crossref_primary_10_1186_s40168_024_01861_6 crossref_primary_10_1038_s42003_023_04430_z crossref_primary_10_1016_j_scitotenv_2023_164108 crossref_primary_10_1128_aem_00726_24 crossref_primary_10_1038_s41396_020_0725_0 crossref_primary_10_1038_s41587_023_01688_w crossref_primary_10_1093_gigascience_giad055 crossref_primary_10_1186_s40793_024_00586_1 crossref_primary_10_1016_j_csbj_2022_06_019 crossref_primary_10_1093_femsec_fiae140 crossref_primary_10_1128_mra_00499_22 crossref_primary_10_1038_s41586_024_07180_y crossref_primary_10_1128_mra_00556_22 crossref_primary_10_1186_s12859_023_05492_w crossref_primary_10_3389_fmicb_2023_1206414 crossref_primary_10_1038_s41467_024_52037_7 crossref_primary_10_15252_embj_2021108287 crossref_primary_10_12688_f1000research_128091_2 crossref_primary_10_1128_MRA_00884_20 crossref_primary_10_1073_pnas_2110968118 crossref_primary_10_12688_f1000research_128091_1 crossref_primary_10_1038_s41598_024_68868_9 crossref_primary_10_1186_s12915_023_01531_3 crossref_primary_10_1007_s00203_023_03711_9 crossref_primary_10_5194_bg_22_1321_2025 crossref_primary_10_3389_fmars_2022_784807 crossref_primary_10_1016_j_chemosphere_2025_144109 crossref_primary_10_1038_s41467_024_47155_1 crossref_primary_10_1093_ismeco_ycae112 crossref_primary_10_1126_sciadv_adr6070 crossref_primary_10_12688_f1000research_152290_2 crossref_primary_10_12688_f1000research_152290_1 crossref_primary_10_1126_sciadv_adi3401 crossref_primary_10_1128_spectrum_04282_22 crossref_primary_10_1038_s43705_023_00254_4 crossref_primary_10_1038_s41592_021_01254_9 crossref_primary_10_1128_msystems_00432_22 crossref_primary_10_1371_journal_pcbi_1010705 crossref_primary_10_3389_fmicb_2025_1533115 crossref_primary_10_1016_j_marpolbul_2023_115747 crossref_primary_10_1093_nargab_lqac007 crossref_primary_10_1093_ismeco_ycae024 crossref_primary_10_1002_ppp_2131 crossref_primary_10_1038_s41467_023_43960_2 crossref_primary_10_1038_s41396_023_01537_3 crossref_primary_10_1016_j_jbiosc_2024_09_006 crossref_primary_10_1093_bioinformatics_btae086 crossref_primary_10_1093_gigascience_giad022 crossref_primary_10_1002_imt2_70001 crossref_primary_10_1038_s41598_023_31626_4 crossref_primary_10_1016_j_jece_2024_114661 crossref_primary_10_1128_msystems_00734_24 crossref_primary_10_1016_j_enzmictec_2025_110619 crossref_primary_10_1016_j_marenvres_2024_106497 crossref_primary_10_1111_mec_16118 crossref_primary_10_1029_2022JE007283 crossref_primary_10_1128_msystems_01282_22 crossref_primary_10_1021_acs_jafc_2c08953 crossref_primary_10_1186_s40793_024_00621_1 crossref_primary_10_3389_fmicb_2022_883495 crossref_primary_10_1038_s41396_023_01453_6 crossref_primary_10_1038_s41467_023_40719_7 crossref_primary_10_1007_s00253_021_11658_4 crossref_primary_10_1371_journal_pcbi_1008716 crossref_primary_10_1186_s40793_025_00689_3 crossref_primary_10_21105_joss_04851 crossref_primary_10_3389_fmicb_2022_869135 crossref_primary_10_1038_s41598_024_72467_z crossref_primary_10_1038_s41598_023_38307_2 crossref_primary_10_3389_fmicb_2022_889788 crossref_primary_10_1097_OLQ_0000000000001821 crossref_primary_10_1016_j_micres_2024_127738 crossref_primary_10_1038_s42003_022_03977_7 crossref_primary_10_1128_mra_00102_24 crossref_primary_10_1128_msystems_00742_23 crossref_primary_10_1111_eva_13687 crossref_primary_10_1007_s11356_024_35287_2 crossref_primary_10_1016_j_csbj_2022_01_018 crossref_primary_10_1093_bioinformatics_btae542 crossref_primary_10_7717_peerj_16695 crossref_primary_10_1016_j_jcmgh_2024_101392 crossref_primary_10_3389_fmicb_2022_955404 crossref_primary_10_1128_msystems_00583_24 crossref_primary_10_1128_msphere_00420_22 |
| Cites_doi | 10.1038/s41467-018-04964-5 10.1038/s41592-018-0046-7 10.1038/nbt.4229 10.1186/s13059-016-1116-8 10.1038/s41467-018-03317-6 10.1038/ismej.2017.126 10.1016/j.cmet.2018.08.005 10.1038/nmeth.4458 10.1186/gb-2004-5-2-r12 10.1016/j.cell.2016.08.007 10.1016/j.jfma.2018.02.005 10.1038/nbt.3960 10.1101/gr.213959.116 10.1093/molbev/msx148 10.1038/s41564-018-0171-1 10.1038/s41586-019-0965-1 10.1038/s41564-017-0012-7 10.1093/nar/gkw929 10.1038/nrmicro3468 10.1186/s13059-016-0997-x 10.1186/1471-2105-11-119 10.1038/nbt.3988 10.1093/nar/gky1085 10.7717/peerj.1319 10.1016/j.ymeth.2016.02.020 10.1093/bioinformatics/btv033 10.1101/gr.186072.114 10.1128/mSystems.00021-16 10.1038/nmeth.2693 10.1101/490078 10.1093/bioinformatics/btv638 10.1093/bioinformatics/btw183 10.7717/peerj.7359 10.1093/bioinformatics/bts480 10.1093/bioinformatics/btv226 10.1038/s41592-018-0176-y |
| ContentType | Journal Article |
| Copyright | The Author(s) 2020 COPYRIGHT 2020 BioMed Central Ltd. 2020. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
| Copyright_xml | – notice: The Author(s) 2020 – notice: COPYRIGHT 2020 BioMed Central Ltd. – notice: 2020. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
| CorporateAuthor | Pacific Northwest National Laboratory (PNNL), Richland, WA (United States) |
| CorporateAuthor_xml | – sequence: 0 name: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States) |
| DBID | C6C AAYXX CITATION ISR 3V. 7QO 7SC 7X7 7XB 88E 8AL 8AO 8FD 8FE 8FG 8FH 8FI 8FJ 8FK ABUWG AEUYN AFKRA ARAPS AZQEC BBNVY BENPR BGLVJ BHPHI CCPQU DWQXO FR3 FYUFA GHDGH GNUQQ HCIFZ JQ2 K7- K9. L7M LK8 L~C L~D M0N M0S M1P M7P P5Z P62 P64 PHGZM PHGZT PIMPY PJZUB PKEHL PPXIY PQEST PQGLB PQQKQ PQUKI PRINS Q9U 7X8 OIOZB OTOTI 5PM ADTOC UNPAY DOA |
| DOI | 10.1186/s12859-020-03585-4 |
| DatabaseName | Springer Nature OA Free Journals CrossRef Gale In Context: Science ProQuest Central (Corporate) Biotechnology Research Abstracts Computer and Information Systems Abstracts ProQuest Health & Medical Collection ProQuest Central (purchase pre-March 2016) Medical Database (Alumni Edition) Computing Database (Alumni Edition) ProQuest Pharma Collection Technology Research Database ProQuest SciTech Collection ProQuest Technology Collection ProQuest Natural Science Journals ProQuest Hospital Collection Hospital Premium Collection (Alumni Edition) ProQuest Central (Alumni) (purchase pre-March 2016) ProQuest Central (Alumni) ProQuest One Sustainability ProQuest Central UK/Ireland Advanced Technologies & Computer Science Collection ProQuest Central Essentials Biological Science Collection ProQuest Central Technology Collection Natural Science Collection ProQuest One Community College ProQuest Central Engineering Research Database Health Research Premium Collection Health Research Premium Collection (Alumni) ProQuest Central Student SciTech Premium Collection ProQuest Computer Science Collection Computer Science Database ProQuest Health & Medical Complete (Alumni) Advanced Technologies Database with Aerospace Biological Sciences Computer and Information Systems Abstracts Academic Computer and Information Systems Abstracts Professional Computing Database Health & Medical Collection (Alumni Edition) Medical Database Biological Science Database Advanced Technologies & Aerospace Database ProQuest Advanced Technologies & Aerospace Collection Biotechnology and BioEngineering Abstracts ProQuest Central Premium ProQuest One Academic Publicly Available Content Database ProQuest Health & Medical Research Collection ProQuest One Academic Middle East (New) ProQuest One Health & Nursing ProQuest One Academic Eastern Edition (DO NOT USE) ProQuest One Applied & Life Sciences ProQuest One Academic ProQuest One Academic UKI Edition ProQuest Central China ProQuest Central Basic MEDLINE - Academic OSTI.GOV - Hybrid OSTI.GOV PubMed Central (Full Participant titles) Unpaywall for CDI: Periodical Content Unpaywall Directory of Open Access Journals (DOAJ) |
| DatabaseTitle | CrossRef Publicly Available Content Database Computer Science Database ProQuest Central Student ProQuest Advanced Technologies & Aerospace Collection ProQuest Central Essentials ProQuest Computer Science Collection Computer and Information Systems Abstracts SciTech Premium Collection ProQuest Central China ProQuest One Applied & Life Sciences ProQuest One Sustainability Health Research Premium Collection Natural Science Collection Health & Medical Research Collection Biological Science Collection ProQuest Central (New) ProQuest Medical Library (Alumni) Advanced Technologies & Aerospace Collection ProQuest Biological Science Collection ProQuest One Academic Eastern Edition ProQuest Hospital Collection ProQuest Technology Collection Health Research Premium Collection (Alumni) Biological Science Database ProQuest Hospital Collection (Alumni) Biotechnology and BioEngineering Abstracts ProQuest Health & Medical Complete ProQuest One Academic UKI Edition Engineering Research Database ProQuest One Academic ProQuest One Academic (New) Technology Collection Technology Research Database Computer and Information Systems Abstracts – Academic ProQuest One Academic Middle East (New) ProQuest Health & Medical Complete (Alumni) ProQuest Central (Alumni Edition) ProQuest One Community College ProQuest One Health & Nursing ProQuest Natural Science Collection ProQuest Pharma Collection ProQuest Central ProQuest Health & Medical Research Collection Biotechnology Research Abstracts Health and Medicine Complete (Alumni Edition) ProQuest Central Korea Advanced Technologies Database with Aerospace ProQuest Computing ProQuest Central Basic ProQuest Computing (Alumni Edition) ProQuest SciTech Collection Computer and Information Systems Abstracts Professional Advanced Technologies & Aerospace Database ProQuest Medical Library ProQuest Central (Alumni) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE - Academic Publicly Available Content Database |
| Database_xml | – sequence: 1 dbid: C6C name: Springer Nature Open Access Journals url: http://www.springeropen.com/ sourceTypes: Publisher – sequence: 2 dbid: DOA name: DOAJ Directory of Open Access Journals url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 3 dbid: UNPAY name: Unpaywall url: https://proxy.k.utb.cz/login?url=https://unpaywall.org/ sourceTypes: Open Access Repository – sequence: 4 dbid: 8FG name: ProQuest Technology Collection url: https://search.proquest.com/technologycollection1 sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1471-2105 |
| EndPage | 8 |
| ExternalDocumentID | oai_doaj_org_article_e5ba32b8279b45268b11b3e0f6edc7ec 10.1186/s12859-020-03585-4 PMC7310028 1646625 A627548322 10_1186_s12859_020_03585_4 |
| GrantInformation_xml | – fundername: European Research Council grantid: ERC-COG-2018 – fundername: Pacific Northwest National Laboratory LDRD program grantid: Microbiomes in Transition Initiative – fundername: ; grantid: Microbiomes in Transition Initiative – fundername: ; grantid: ERC-COG-2018 |
| GroupedDBID | --- 0R~ 23N 2WC 53G 5VS 6J9 7X7 88E 8AO 8FE 8FG 8FH 8FI 8FJ AAFWJ AAJSJ AAKPC AASML ABDBF ABUWG ACGFO ACGFS ACIHN ACIWK ACPRK ACUHS ADBBV ADMLS ADUKV AEAQA AENEX AEUYN AFKRA AFPKN AFRAH AHBYD AHMBA AHYZX ALMA_UNASSIGNED_HOLDINGS AMKLP AMTXH AOIJS ARAPS AZQEC BAPOH BAWUL BBNVY BCNDV BENPR BFQNJ BGLVJ BHPHI BMC BPHCQ BVXVI C6C CCPQU CS3 DIK DU5 DWQXO E3Z EAD EAP EAS EBD EBLON EBS EMB EMK EMOBN ESX F5P FYUFA GNUQQ GROUPED_DOAJ GX1 HCIFZ HMCUK HYE IAO ICD IHR INH INR ISR ITC K6V K7- KQ8 LK8 M1P M48 M7P MK~ ML0 M~E O5R O5S OK1 OVT P2P P62 PGMZT PHGZM PHGZT PIMPY PJZUB PPXIY PQGLB PQQKQ PROAC PSQYO PUEGO RBZ RNS ROL RPM RSV SBL SOJ SV3 TR2 TUS UKHRP W2D WOQ WOW XH6 XSB AAYXX CITATION 3V. 7QO 7SC 7XB 8AL 8FD 8FK FR3 JQ2 K9. L7M L~C L~D M0N P64 PKEHL PQEST PQUKI PRINS Q9U 7X8 -A0 ACRMQ ADINQ ALIPV C24 OIOZB OTOTI 5PM 123 2VQ 4.4 ADRAZ ADTOC AHSBF C1A EJD H13 IPNFZ RIG UNPAY |
| ID | FETCH-LOGICAL-c711t-e454e58ecb7b5fb36d5c3ba2edb283401f03955a471254543ae29a50a63fba693 |
| IEDL.DBID | UNPAY |
| ISSN | 1471-2105 |
| IngestDate | Fri Oct 03 12:40:02 EDT 2025 Sun Oct 26 04:09:43 EDT 2025 Tue Sep 30 17:06:28 EDT 2025 Thu Dec 05 06:32:36 EST 2024 Fri Sep 05 11:21:19 EDT 2025 Tue Oct 07 05:17:02 EDT 2025 Mon Oct 20 22:07:56 EDT 2025 Mon Oct 20 16:22:46 EDT 2025 Thu Oct 16 14:47:46 EDT 2025 Wed Oct 01 04:15:35 EDT 2025 Thu Apr 24 23:10:04 EDT 2025 Sat Sep 06 07:27:25 EDT 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 1 |
| Keywords | Analysis workflow Metagenome-assembled genomes Metagenomics Annotation |
| Language | English |
| License | Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. cc-by |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c711t-e454e58ecb7b5fb36d5c3ba2edb283401f03955a471254543ae29a50a63fba693 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 USDOE AC05-76RL01830 PNNL-SA-143152 |
| ORCID | 0000-0003-4456-517X 000000034456517X |
| OpenAccessLink | https://proxy.k.utb.cz/login?url=https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03585-4 |
| PMID | 32571209 |
| PQID | 2424712574 |
| PQPubID | 44065 |
| PageCount | 8 |
| ParticipantIDs | doaj_primary_oai_doaj_org_article_e5ba32b8279b45268b11b3e0f6edc7ec unpaywall_primary_10_1186_s12859_020_03585_4 pubmedcentral_primary_oai_pubmedcentral_nih_gov_7310028 osti_scitechconnect_1646625 proquest_miscellaneous_2416263168 proquest_journals_2424712574 gale_infotracmisc_A627548322 gale_infotracacademiconefile_A627548322 gale_incontextgauss_ISR_A627548322 crossref_citationtrail_10_1186_s12859_020_03585_4 crossref_primary_10_1186_s12859_020_03585_4 springer_journals_10_1186_s12859_020_03585_4 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2020-06-22 |
| PublicationDateYYYYMMDD | 2020-06-22 |
| PublicationDate_xml | – month: 06 year: 2020 text: 2020-06-22 day: 22 |
| PublicationDecade | 2020 |
| PublicationPlace | London |
| PublicationPlace_xml | – name: London – name: United States |
| PublicationTitle | BMC bioinformatics |
| PublicationTitleAbbrev | BMC Bioinformatics |
| PublicationYear | 2020 |
| Publisher | BioMed Central BioMed Central Ltd Springer Nature B.V BMC |
| Publisher_xml | – sequence: 0 name: BioMed Central – name: BioMed Central – name: BioMed Central Ltd – name: Springer Nature B.V – name: BMC |
| References | DH Parks (3585_CR31) 2015; 25 RD Stewart (3585_CR13) 2018; 9 S Kurtz (3585_CR33) 2004; 5 3585_CR11 D Hyatt (3585_CR34) 2010; 11 JR Kultima (3585_CR16) 2016; 32 J Koster (3585_CR20) 2012; 28 DD Kang (3585_CR27) 2019; 7 JI Prosser (3585_CR2) 2015; 13 J Huerta-Cepas (3585_CR38) 2019; 47 A Almeida (3585_CR10) 2019; 568 S Narayanasamy (3585_CR17) 2016; 17 B Bushnell (3585_CR23) 2019 J Huerta-Cepas (3585_CR37) 2017; 34 CMK Sieber (3585_CR30) 2018; 3 D Li (3585_CR25) 2015; 31 S Fabbiano (3585_CR40) 2018; 28 IA Chen (3585_CR14) 2017; 45 BD Ondov (3585_CR32) 2016; 17 3585_CR19 3585_CR7 S Sunagawa (3585_CR9) 2013; 10 PI Costea (3585_CR3) 2017; 35 3585_CR21 M Steinegger (3585_CR36) 2017; 35 WK Wu (3585_CR5) 2019; 118 B Gruning (3585_CR22) 2018; 15 3585_CR4 A Sczyrba (3585_CR6) 2017; 14 DH Parks (3585_CR39) 2018; 36 H Mirebrahim (3585_CR18) 2015; 31 AM Eren (3585_CR15) 2015; 3 S Nurk (3585_CR24) 2017; 27 YW Wu (3585_CR28) 2016; 32 M Steinegger (3585_CR35) 2018; 9 MR Olm (3585_CR29) 2017; 11 DH Parks (3585_CR12) 2017; 2 S Nayfach (3585_CR1) 2016; 166 3585_CR26 EA Franzosa (3585_CR8) 2018; 15 |
| References_xml | – volume: 9 start-page: 2542 issue: 1 year: 2018 ident: 3585_CR35 publication-title: Nat Commun doi: 10.1038/s41467-018-04964-5 – volume: 15 start-page: 475 issue: 7 year: 2018 ident: 3585_CR22 publication-title: Nat Methods doi: 10.1038/s41592-018-0046-7 – volume: 36 start-page: 996 issue: 10 year: 2018 ident: 3585_CR39 publication-title: Nat Biotechnol doi: 10.1038/nbt.4229 – volume: 17 start-page: 260 issue: 1 year: 2016 ident: 3585_CR17 publication-title: Genome Biol doi: 10.1186/s13059-016-1116-8 – volume: 9 start-page: 870 issue: 1 year: 2018 ident: 3585_CR13 publication-title: Nat Commun doi: 10.1038/s41467-018-03317-6 – volume: 11 start-page: 2864 issue: 12 year: 2017 ident: 3585_CR29 publication-title: ISME J doi: 10.1038/ismej.2017.126 – volume: 28 start-page: 907 issue: 6 year: 2018 ident: 3585_CR40 publication-title: Cell Metab doi: 10.1016/j.cmet.2018.08.005 – volume: 14 start-page: 1063 issue: 11 year: 2017 ident: 3585_CR6 publication-title: Nat Methods doi: 10.1038/nmeth.4458 – volume: 5 start-page: R12 issue: 2 year: 2004 ident: 3585_CR33 publication-title: Genome Biol doi: 10.1186/gb-2004-5-2-r12 – volume: 166 start-page: 1103 issue: 5 year: 2016 ident: 3585_CR1 publication-title: Cell. doi: 10.1016/j.cell.2016.08.007 – volume: 118 start-page: 545 issue: 2 year: 2019 ident: 3585_CR5 publication-title: J Formos Med Assoc doi: 10.1016/j.jfma.2018.02.005 – volume: 35 start-page: 1069 issue: 11 year: 2017 ident: 3585_CR3 publication-title: Nat Biotechnol doi: 10.1038/nbt.3960 – volume: 27 start-page: 824 issue: 5 year: 2017 ident: 3585_CR24 publication-title: Genome Res doi: 10.1101/gr.213959.116 – volume: 34 start-page: 2115 issue: 8 year: 2017 ident: 3585_CR37 publication-title: Mol Biol Evol doi: 10.1093/molbev/msx148 – volume: 3 start-page: 836 issue: 7 year: 2018 ident: 3585_CR30 publication-title: Nat Microbiol doi: 10.1038/s41564-018-0171-1 – volume: 568 start-page: 499 issue: 7753 year: 2019 ident: 3585_CR10 publication-title: Nature. doi: 10.1038/s41586-019-0965-1 – volume: 2 start-page: 1533 issue: 11 year: 2017 ident: 3585_CR12 publication-title: Nat Microbiol doi: 10.1038/s41564-017-0012-7 – volume: 45 start-page: D507 issue: D1 year: 2017 ident: 3585_CR14 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkw929 – ident: 3585_CR19 – volume-title: BBTools year: 2019 ident: 3585_CR23 – volume: 13 start-page: 439 issue: 7 year: 2015 ident: 3585_CR2 publication-title: Nat Rev Microbiol doi: 10.1038/nrmicro3468 – volume: 17 start-page: 132 issue: 1 year: 2016 ident: 3585_CR32 publication-title: Genome Biol doi: 10.1186/s13059-016-0997-x – volume: 11 start-page: 119 year: 2010 ident: 3585_CR34 publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-11-119 – volume: 35 start-page: 1026 issue: 11 year: 2017 ident: 3585_CR36 publication-title: Nat Biotechnol doi: 10.1038/nbt.3988 – volume: 47 start-page: D309 issue: D1 year: 2019 ident: 3585_CR38 publication-title: Nucleic Acids Res doi: 10.1093/nar/gky1085 – volume: 3 year: 2015 ident: 3585_CR15 publication-title: PeerJ. doi: 10.7717/peerj.1319 – ident: 3585_CR26 doi: 10.1016/j.ymeth.2016.02.020 – ident: 3585_CR7 – volume: 31 start-page: 1674 issue: 10 year: 2015 ident: 3585_CR25 publication-title: Bioinformatics. doi: 10.1093/bioinformatics/btv033 – volume: 25 start-page: 1043 issue: 7 year: 2015 ident: 3585_CR31 publication-title: Genome Res doi: 10.1101/gr.186072.114 – ident: 3585_CR4 doi: 10.1128/mSystems.00021-16 – volume: 10 start-page: 1196 issue: 12 year: 2013 ident: 3585_CR9 publication-title: Nat Methods doi: 10.1038/nmeth.2693 – ident: 3585_CR11 doi: 10.1101/490078 – volume: 32 start-page: 605 issue: 4 year: 2016 ident: 3585_CR28 publication-title: Bioinformatics. doi: 10.1093/bioinformatics/btv638 – volume: 32 start-page: 2520 issue: 16 year: 2016 ident: 3585_CR16 publication-title: Bioinformatics. doi: 10.1093/bioinformatics/btw183 – ident: 3585_CR21 – volume: 7 year: 2019 ident: 3585_CR27 publication-title: PeerJ. doi: 10.7717/peerj.7359 – volume: 28 start-page: 2520 issue: 19 year: 2012 ident: 3585_CR20 publication-title: Bioinformatics. doi: 10.1093/bioinformatics/bts480 – volume: 31 start-page: i9 issue: 12 year: 2015 ident: 3585_CR18 publication-title: Bioinformatics. doi: 10.1093/bioinformatics/btv226 – volume: 15 start-page: 962 issue: 11 year: 2018 ident: 3585_CR8 publication-title: Nat Methods doi: 10.1038/s41592-018-0176-y |
| SSID | ssj0017805 |
| Score | 2.6250737 |
| Snippet | Background
Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the... Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data... Background Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the... Background: Metagenomics and metatranscriptomics studies provide valuable insight into the composition and function of microbial populations from diverse... Abstract Background Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments;... |
| SourceID | doaj unpaywall pubmedcentral osti proquest gale crossref springer |
| SourceType | Open Website Open Access Repository Aggregation Database Enrichment Source Index Database Publisher |
| StartPage | 1 |
| SubjectTerms | Algorithms Analysis Analysis workflow Annotation Annotations Assembly Automation BASIC BIOLOGICAL SCIENCES Bioinformatics Biomedical and Life Sciences Computational Biology/Bioinformatics Computer Appl. in Life Sciences Data processing Gene mapping Genes Genomes Genomics High performance computing Life Sciences Mapping Metagenome-assembled genomes Metagenomics Microarrays Microorganisms Nucleotide sequence Phylogenetics Quality control Sequence analysis Software Source code Taxonomy Workflow Workflow software |
| SummonAdditionalLinks | – databaseName: Directory of Open Access Journals (DOAJ) dbid: DOA link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV3db9MwELdQJQQ8ID5F2EAGIfFAo8VOHDu8FcQ0EPBAN2lvlu3YYyJNJtpq6n_PXb5YeBg88FCpis-NfHc-3_XOvyPklZOlSnIfYp4GCFCYZbFRYAxLOIoZ9-BQZHg5-cvX_Ogk-3QqTq-0-sKasA4euGPcgRfWpNwqLguL7bCVZcymPgm5L530Dq1vooohmOrzB4jUP1yRUfnBmiFOW4yhUpKCgxxnk2OoResfbfKsgc01cTj_LJccc6Z3yK1tfWF2l6aqrhxLh_fI3d6fpItuHffJDV8_IDe7DpO7h8Qvjj8vlm-pocva_PAr-FAsxQpVc0nBX6XgO_uVrXZzauq66fLy-L2kiN66OncUQmf874Q2ga78xrSPPR1KsCmWmD4iJ4cfjt8fxX1nhdhJxjaxz0TmhfLOSiuCTfNSuNQa7ksL7gaEXCFJCyEMnFwQQIosNZ4XRiQmT4M1eZE-JrO6qf0TQqUJwkFcEwImXHliVVDcJjIkTgabFRFhA6O162HHsftFpdvwQ-W6E44G4ehWODqLyJtxzkUHunEt9TuU30iJgNntA1Aj3auR_psaReQlSl8jJEaNNTdnZrte64_Lb3qBQM4ZWr6IvO6JQgNrcKa_wgCcQBStCeX-hBL2rJsM76GSafByEKrXYU2T22jEeoN4FCYPuqd7i7LWeI0HpSFhvS_GYfxdrJKrfbNFGobgQixXEZETnZ0wZzpSn39vUcUlpno4zJwP2v375dcxfz7ugH-Q1dP_Ias9cpu3WzmPOd8ns83PrX8GruHGPm-twC9QWVwa priority: 102 providerName: Directory of Open Access Journals – databaseName: ProQuest Central dbid: BENPR link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV3da9swEBddytj2MPZV5rYb2hjsYTG15A85gzHS0dKNLYymhb4JSZa6MsdOG4eS_353ju3Oewh7MATr5GCd7nTnu_sdIe-MyNIgsc7noQMHhWnmqxSUYQZHMeMWDIoIi5N_TJKT8-jbRXyxRSZtLQymVbY6sVbUWWnwG_kBljEIOI1F9Hl-7WPXKIyuti00VNNaIftUQ4zdI9sckbEGZPvwaPLztIsrIIJ_WzqTJgcLhvhtPrpQQQiGsx_1jqcaxb_T1YMShK5niP6bRtnFUh-RB8tirla3Ks__Oq6On5DHjZ1Jx-uN8ZRs2eIZub_uPLl6Tuz47Pt4-pEqOi3UbzuDi2KKlsvLWwp2LAWb2s50vhpSVRTlOl6PvzOKqK6zK0PBpcZvKrR0dGYrVd-2tE3Npph6-oKcHx-dfTnxm44LvhGMVb6N4sjGqTVa6NjpMMliE2rFbabBDAFXzAXhKI5VzQmgDZXlIxUHKgmdVsko3CGDoizsS0KFcrEBf8c5DMTyQKcu5ToQLjDC6WjkEdYutDQNHDl2xchl7ZakiVwzRwJzZM0cGXnkQzdnvgbj2Eh9iPzrKBFIu75R3lzKRi6ljbUKuU65GGnstp5qxnRoA5cAX4U1HnmL3JcIlVFgLs6lWi4W8uv0VI4R4DlCjeiR9w2RK-EdjGpKG2AlEF2rR7nfowRZNr3hPdxkEqwfhPA1mOtkKokYcOCnwuR278lG0yzknVx45E03jM_F7LnClkukYQg6xJLUI6K3Z3uL0x8prn7VaOMCQ0AcZg7b3X3355sWf9hJwH_wanfzq-2Rh7wW0sTnfJ8MqpulfQXGYKVfNxL-Bw2MWUM priority: 102 providerName: ProQuest – databaseName: Scholars Portal Journals: Open Access dbid: M48 link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV3db9MwELdGEQIeEJ-ibCCDkHiggdiJ4wQJoYKYBmI80FXam2W79piWJlubavS_5y5NMoKmaQ-RovicKvdh39V3vyPktZWzNEycD3jkIUBhhgU6hcVwBlsx4w4cihiLk_d_JnvT-PuhONwibbujhoHLS0M77Cc1XeTv_pytP4HBf6wNPk3eLxmisAUYCIURuL9BfIPchJ0qw1YO-_HFqQLi99fVRpIFEOqItojm0nf0Nqoaz79btQclmF_PJf0_obI7Vb1Lbq-KU70-13n-z8a1e5_cazxOOt6oyAOy5YqH5NamB-X6EXHjgx_jyQeq6aTQJ24OF8VkLZ-X5xQ8WgretZubfD2iuijKzck93s8o4rvOjy2F4Br_XaGlp3NX6fqxo22SNsUk1Mdkuvv14Mte0PReCKxkrApcLGInUmeNNMKbKJkJGxnN3cyAQwJBmQ-jTAgNrIQQU8SRdjzTItRJ5I1OsugJGRRl4Z4SKrUXFiIf7_FIlocm9Sk3ofShld7E2ZCwltHKNsDk2B8jV3WAkiZqIxwFwlG1cFQ8JG-7OacbWI4rqT-j_DpKhNSuH5SLI9VYqHLC6IiblMvMYN_11DBmIhf6BOQqnR2SVyh9haAZBWblHOnVcqm-TX6pMUI9x7g2DsmbhsiX8A1WN0UOwAnE2epR7vQowaptb3gblUyBH4RgvhaznmylEA0OIlaY3Oqeak1GYaEPSkPC977shvG9mEdXuHKFNAzhh1iSDons6WyPOf2R4vh3jTsu8TCIw8xRq90XP34V80edBVxDVs-uzcFtcofX9poEnO-QQbVYuefgIVbmRW32fwEva1vl priority: 102 providerName: Scholars Portal – databaseName: Springer Nature OA Free Journals dbid: C6C link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV3db9MwELegCDEeEJ9a2UAGIfFAo8VObKe8lYlpIOCBbtLeLNu1YaJ1Jppq6n_PXb5YEJrgIVIUn1PFd-e76939TMgrpxZFKn1IeBYgQGGWJaaAzXABpphxDw5Fjs3Jn7_I49P845k4a2FysBfmav6eFfJgzRBhLcEgJ83AtU3ym-QWGClZJ2blYZ8xQGz-rinmr_MGhqfG5-934VEJ6jRwMf8skOyzpHfJnU28MNtLs1xeMURH98m91oOks4blD8gNHx-S282ZkttHxM9OPs3mb6mh82h--BVcFIuvwrK8pOChUvCW_coutxNqYiybTDzeLyjita7OHYVgGf8toWWgK1-Z-rGnXdE1xaLSx-T06P3J4XHSnqWQOMVYlfhc5F4U3lllRbCZXAiXWcP9woKDAUFWSLOpEAZsFYSMIs-M51MjUiOzYI2cZk_IKJbR7xKqTBAOIpkQMMXKU1uEgttUhdSpYPPpmLBuobVrgcbxvIulrgOOQuqGORqYo2vm6HxM3vRzLhqYjWup3yH_ekqEyK4fgOToVuO0F9Zk3BZcTS2eo15Yxmzm0yCBr8q7MXmJ3NcIghGxyuab2azX-sP8q54hdHOOe92YvG6JQgnf4EzbtAArgbhZA8r9ASVoqRsM76GQafBrEJzXYRWTqzSiu0EECpM72dPtHrLW2LiD3FDwvS_6YXwv1sVFX26QhiGcEJPFmKiBzA4WZzgSz7_XOOIKkzscZk466f7949ct_qTXgH_g1dP_e_se2eG10sqE830yqn5u_DNw-yr7vNb3X3vOS6k priority: 102 providerName: Springer Nature |
| Title | ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data |
| URI | https://link.springer.com/article/10.1186/s12859-020-03585-4 https://www.proquest.com/docview/2424712574 https://www.proquest.com/docview/2416263168 https://www.osti.gov/servlets/purl/1646625 https://pubmed.ncbi.nlm.nih.gov/PMC7310028 https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03585-4 https://doaj.org/article/e5ba32b8279b45268b11b3e0f6edc7ec |
| UnpaywallVersion | publishedVersion |
| Volume | 21 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVADU databaseName: BioMedCentral customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: RBZ dateStart: 20000101 isFulltext: true titleUrlDefault: https://www.biomedcentral.com/search/ providerName: BioMedCentral – providerCode: PRVAFT databaseName: Open Access Digital Library customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: KQ8 dateStart: 20000101 isFulltext: true titleUrlDefault: http://grweb.coalliance.org/oadl/oadl.html providerName: Colorado Alliance of Research Libraries – providerCode: PRVAFT databaseName: Open Access Digital Library customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: KQ8 dateStart: 20000701 isFulltext: true titleUrlDefault: http://grweb.coalliance.org/oadl/oadl.html providerName: Colorado Alliance of Research Libraries – providerCode: PRVAON databaseName: DOAJ Directory of Open Access Journals customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: DOA dateStart: 20000101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVEBS databaseName: EBSCOhost Academic Search Ultimate customDbUrl: https://search.ebscohost.com/login.aspx?authtype=ip,shib&custid=s3936755&profile=ehost&defaultdb=asn eissn: 1471-2105 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: ABDBF dateStart: 20000101 isFulltext: true titleUrlDefault: https://search.ebscohost.com/direct.asp?db=asn providerName: EBSCOhost – providerCode: PRVEBS databaseName: Inspec with Full Text customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: ADMLS dateStart: 20000101 isFulltext: true titleUrlDefault: https://www.ebsco.com/products/research-databases/inspec-full-text providerName: EBSCOhost – providerCode: PRVBFR databaseName: Free Medical Journals customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: DIK dateStart: 20000101 isFulltext: true titleUrlDefault: http://www.freemedicaljournals.com providerName: Flying Publisher – providerCode: PRVFQY databaseName: GFMER Free Medical Journals customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: GX1 dateStart: 0 isFulltext: true titleUrlDefault: http://www.gfmer.ch/Medical_journals/Free_medical.php providerName: Geneva Foundation for Medical Education and Research – providerCode: PRVHPJ databaseName: ROAD: Directory of Open Access Scholarly Resources customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: M~E dateStart: 20000101 isFulltext: true titleUrlDefault: https://road.issn.org providerName: ISSN International Centre – providerCode: PRVAQN databaseName: PubMed Central customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: RPM dateStart: 20000101 isFulltext: true titleUrlDefault: https://www.ncbi.nlm.nih.gov/pmc/ providerName: National Library of Medicine – providerCode: PRVPQU databaseName: Health & Medical Collection (Proquest) customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: 7X7 dateStart: 20090101 isFulltext: true titleUrlDefault: https://search.proquest.com/healthcomplete providerName: ProQuest – providerCode: PRVPQU databaseName: ProQuest Central customDbUrl: http://www.proquest.com/pqcentral?accountid=15518 eissn: 1471-2105 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: BENPR dateStart: 20090101 isFulltext: true titleUrlDefault: https://www.proquest.com/central providerName: ProQuest – providerCode: PRVPQU databaseName: ProQuest Technology Collection customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: 8FG dateStart: 20090101 isFulltext: true titleUrlDefault: https://search.proquest.com/technologycollection1 providerName: ProQuest – providerCode: PRVFZP databaseName: Scholars Portal Journals: Open Access customDbUrl: eissn: 1471-2105 dateEnd: 20250131 omitProxy: true ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: M48 dateStart: 20000701 isFulltext: true titleUrlDefault: http://journals.scholarsportal.info providerName: Scholars Portal – providerCode: PRVAVX databaseName: Springer Nature HAS Fully OA customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: AAJSJ dateStart: 20001201 isFulltext: true titleUrlDefault: https://www.springernature.com providerName: Springer Nature – providerCode: PRVAVX databaseName: Springer Nature Open Access Journals customDbUrl: eissn: 1471-2105 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0017805 issn: 1471-2105 databaseCode: C6C dateStart: 20000112 isFulltext: true titleUrlDefault: http://www.springeropen.com/ providerName: Springer Nature |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV3db9MwELe2Tgh44BtRNiqDkHig2fLlOOUtm1ZGxaZpXaXyZNmOPaa1yVhbTeWv5y4fZZnQBBIPTSPnnCjnu_NdfPczIe81T2M3MtbxAwsBiqc8R8ZgDFOYij3fgEMRYnHy4VF0MAoHYzZeI8d1LYyaanWeV6ChCFS8fbMMfVLYbjjRFzuXqS1VPo52Zh7isDkYCrkBOMBOuE42IgbeeYtsjI6Ok29FkRH3HIhwWF0788eOjfmpgPFfGetWDlrX8ERv51GuFlMfkvuL7FIur-VkcmO-6j8mP-o3LdNULrYXc7Wtf94CgfyfrHhCHlXOLU1KaXxK1kz2jNwrt7tcPicmOf2aDD9RSYeZvDBT-FHMC7OT_JrC8yk48maqJssulVmWl0kCeJ5ShJKdnmsKcTx-yKG5pVMzl0WzoXU-OMV81xdk1N8_3Ttwqm0eHM09b-6YkIWGxUYrrphVQZQyHSjpm1SB7wPxn3WDHmMShg-iWRYG0vg9yVwZBVbJqBe8JK0sz8wrQrm0TEOQZS2u_vquim3sK5dbV3Orwl6bePXgCl1hoONWHBNRxEJxJEr2CWCfKNgnwjb5uOpzWSKA3Em9izKzokT07qIhvzoTlTEQhikZ-Cr2eU_hFu-x8jwVGNdGMLrc6DZ5hxInEJ8jwwSgM7mYzcSX4YlIEFU6RDPcJh8qIpujGMiqngI4gZBeDcqtBiUYEN24vImCLcDlQtxgjQlWei4QeA6CY-hcy7uozNtMYE0RjgaH9327uoz3xZS9zOQLpPEQ6ciL4jbhDT1pMKd5JTv_XkCcc1x38qFnt9ao3w-_i_ndldb9xVi9_jfyTfLAL9Qqcnx_i7TmVwvzBjzSueqQdT7mcIz7nztkI0kGwwH87-4fHZ9A61601ym-9cDxMIw7lUn6BXGvifE |
| linkProvider | Unpaywall |
| linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV1bb9MwFLamIjR4QFxF2ACDQDywaIlzcYqEULlMLev2QDupb8Z27DHRJmVtVfVP8Rs5J7cRHipe9lApio8bxeceH3-HkFeap4kXG-uywEKC4ivflQkYwxRcsc8MBBQhHk4-OY37Z-HXSTTZIb_rszBYVlnbxMJQp7nGb-SHeIyBgzfm4Yf5Lxe7RuHuat1CoxSLY7NZQ8q2eD_4DPx9zdjRl_Gnvlt1FXA19_2la8IoNFFitOIqsiqI00gHSjKTKnC1kG5YL-hGkSyeBrSBNKwrI0_GgVUyRvAlMPk3wgBsCegPnzQJno_9AeqDOUl8uPARHc7FBM0LICx3w5bzK3oENJ6gk4NKt8Lcf4s0m53a22R3lc3lZi2n07-c4dFdcqeKYmmvFLt7ZMdk98nNsq_l5gExvfGwN3pHJR1l8qeZwY9iAZid5msKUTKFiN3M1HRzQGWW5WU1AF6nFDFjZxeaQsKOX2xobunMLGVx29C68JtiYetDcnYtK_-IdLI8M48J5dJGGrIpa3Gbl3kqsQlTHree5laFXYf49UILXYGdY8-NqSiSniQWJXMEMEcUzBGhQ942c-Yl1MdW6o_Iv4YSYbqLG_nluai0XphIyYCphPGuwl7uifJ9FRjPxsBXbrRDXiL3BQJxZFjpcy5Xi4UYjL6JHsJHh2hvHfKmIrI5vIOW1cEJWAnE7mpR7rcowVLo1vAeCpmA2AoBgjVWUumlQIQ5yIJhci17orJjC3GldQ550Qzj_2JtXmbyFdL4CGnkx4lDeEtmW4vTHskufhRY5hw3mBjMPKil--rh2xb_oNGA_-DVk-2v9pzs9scnQzEcnB7vkVusUNjYZWyfdJaXK_MUws6lelboOiXfr9u4_AGLH482 |
| linkToPdf | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV3db9MwELegiK8HxKcoG2AQEg80Wux8OOWtFKoNxoTYJu3Nsh17TLROtaaa-t9zly8WhCZ4iBTF51Tx3dl3vbvfEfLGiDwLU-sCHjlwUJhmgcpgM8zhKGbcgkERY3Hy14N09zj-fJKcXKrir7Ld25BkXdOAKE2-3FnmrlbxLN1ZMcRdC9D1CSMweIP4OrkRw-mGPQym6bSLIyBif1sq89d5veOoQu3v9uZBAUrWMzz_TJvsYqd3ye21X6rNhZrPLx1Ps_vkXmNX0kktCA_INesfkpt1p8nNI2InR_uTw_dU0UOvftoFXBRTsty8uKBgt1Kwoe1Czzcjqrwv6vg83ucUUVwXZ4aCC43_odDC0YUtVfXY0jYVm2Kq6WNyPPt0NN0Nmg4LgRGMlYGNk9gmmTVa6MTpKM0TE2nFba7B7ADXy4XROEkUnGDgSCZxpCwfqyRUaeS0SsfREzLwhbdPCRXKJQb8G-cw8MpDnbmM61C40Ain4_GQsHahpWngx7ELxlxWbkiWypo5EpgjK-bIeEjedXOWNfjGldQfkH8dJQJnVw-K81PZ6KG0iVYR1xkXY43d1TPNmI5s6FLgq7BmSF4j9yVCY3jMvTlV69VK7h1-lxMEdI5xBxyStw2RK-AbjGpKGWAlEE2rR7ndowTdNb3hLRQyCdYOQvYazG0ypUTMN_BLYXIre7LZWVYSy3mQGwK-91U3jO_FbDlvizXSMAQZYmk2JKIns73F6Y_4sx8VurjAkA-HmaNWun__-FWLP-o04B949ez_3v6S3Pr2cSb39w6-bJE7vNLfNOB8mwzK87V9DnZhqV9Uqv8LnVBW3w |
| linkToUnpaywall | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV3db9MwELdGJwQ88DlE2UAGIfFA08VJnKS8FcQ0EEwTXaXxZNmOPaqmSVlTTeWv5y5fLBOaQOKhUhSfG-W-fBff_UzIKx0lsRsa63i-hQSFKebIGJxhAksx8wwEFAE2J385Cg-nwadTfrpFjpteGLXQapbXoKEIVDy83Iaelr4bLvR8f5nYyuTjcH_FEIfNwVTI9SEAdoIbZDvkEJ33yPb06Hj8rWwyipgDGQ5vemf-OLGzPpUw_q2z7uVgdZ1I9GodZbuZeofcWmdLubmQaXppvTq4R340b1qVqcyH60IN9c8rIJD_kxX3yd06uKXjShsfkC2TPSQ3q-MuN4-IGZ98Hk_eUkknmZybBfwo1oXZNL-g8HwKgbxZqHQzoDLL8qpIAK8TilCyi5mmkMfjhxyaW7owhSxvG9rUg1Osd90h04MPJ-8PnfqYB0dHjBWOCXhgeGy0ihS3yg8Trn0lPZMoiH0g_7OuP-Jcgvggm-WBL403ktyVoW-VDEf-Y9LL8sw8ITSSlmtIsqzF3V_PVbGNPeVG1tWRVcGoT1gjXKFrDHQ8iiMVZS4Uh6JinwD2iZJ9IuiTN-2cZYUAci31O9SZlhLRu8sb-fmZqJ2BMFxJ31OxF40UHvEeK8aUb1wbgnQjo_vkJWqcQHyODAuAzuR6tRIfJ1_FGFGlA3TDffK6JrI5qoGs-ymAEwjp1aHc61CCA9Gd4V1UbAEhF-IGayyw0oVA4DlIjmFyo--idm8rgT1FKI0I3vdFO4z_iyV7mcnXSMMQ6YiFcZ9EHTvpMKc7ks2-lxDnEe47eTBz0FjU74dfx_xBa3V_Iaun_0a-S257pVmFjuftkV5xvjbPICIt1PPayfwCaIuCUg |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=ATLAS%3A+a+Snakemake+workflow+for+assembly%2C+annotation%2C+and+genomic+binning+of+metagenome+sequence+data&rft.jtitle=BMC+bioinformatics&rft.au=Kieser%2C+Silas&rft.au=Brown%2C+Joseph&rft.au=Zdobnov%2C+Evgeny+M&rft.au=Trajkovski%2C+Mirko&rft.date=2020-06-22&rft.pub=BioMed+Central+Ltd&rft.issn=1471-2105&rft.eissn=1471-2105&rft.volume=21&rft.issue=1&rft_id=info:doi/10.1186%2Fs12859-020-03585-4&rft.externalDocID=A627548322 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1471-2105&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1471-2105&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1471-2105&client=summon |