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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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      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\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/metagenome-atlas\/atlas\">https:\/\/github.com\/metagenome-atlas\/atlas<\/jats:ext-link>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-020-03585-4","type":"journal-article","created":{"date-parts":[[2020,6,22]],"date-time":"2020-06-22T06:02:55Z","timestamp":1592805775000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":175,"title":["ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data"],"prefix":"10.1186","volume":"21","author":[{"given":"Silas","family":"Kieser","sequence":"first","affiliation":[]},{"given":"Joseph","family":"Brown","sequence":"additional","affiliation":[]},{"given":"Evgeny M.","family":"Zdobnov","sequence":"additional","affiliation":[]},{"given":"Mirko","family":"Trajkovski","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4456-517X","authenticated-orcid":false,"given":"Lee Ann","family":"McCue","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,6,22]]},"reference":[{"issue":"5","key":"3585_CR1","doi-asserted-by":"publisher","first-page":"1103","DOI":"10.1016\/j.cell.2016.08.007","volume":"166","author":"S Nayfach","year":"2016","unstructured":"Nayfach S, Pollard KS. 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