{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T00:50:05Z","timestamp":1740099005856,"version":"3.37.3"},"posted":{"date-parts":[[2017,3,2]]},"group-title":"PeerJ Preprints","reference-count":0,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2017,3,2]],"date-time":"2017-03-02T00:00:00Z","timestamp":1488412800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multi-omics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein-coding open reading frames (ORFs) rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.<\/jats:p>","DOI":"10.7287\/peerj.preprints.2843v1","type":"posted-content","created":{"date-parts":[[2018,1,13]],"date-time":"2018-01-13T06:55:08Z","timestamp":1515826508000},"source":"Crossref","is-referenced-by-count":12,"title":["ATLAS (Automatic Tool for Local Assembly Structures) - a comprehensive infrastructure for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data"],"prefix":"10.7287","author":[{"given":"Richard Allen","family":"White III","sequence":"first","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA"}]},{"given":"Joseph","family":"Brown","sequence":"additional","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA"}]},{"given":"Sean","family":"Colby","sequence":"additional","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA"}]},{"given":"Christopher C","family":"Overall","sequence":"additional","affiliation":[{"name":"Department of Neuroscience, University of Virginia, Charlottesville, Virginia, United States"}]},{"given":"Joon-Yong","family":"Lee","sequence":"additional","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7276-9009","authenticated-orcid":true,"given":"Jeremy","family":"Zucker","sequence":"additional","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9512-1395","authenticated-orcid":true,"given":"Kurt R","family":"Glaesemann","sequence":"additional","affiliation":[{"name":"Infomation technology, High Performance Computing (HPC) and Cloud services, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA"}]},{"given":"Christer","family":"Jansson","sequence":"additional","affiliation":[{"name":"Environmental and Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA"}]},{"given":"Janet K","family":"Jansson","sequence":"additional","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA"}]}],"member":"4443","container-title":[],"original-title":[],"link":[{"URL":"https:\/\/peerj.com\/preprints\/2843v1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/preprints\/2843v1.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/preprints\/2843v1.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/preprints\/2843v1.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,12,23]],"date-time":"2019-12-23T16:49:46Z","timestamp":1577119786000},"score":1,"resource":{"primary":{"URL":"https:\/\/peerj.com\/preprints\/2843v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,3,2]]},"references-count":0,"aliases":["10.7287\/peerj.preprints.2843"],"URL":"https:\/\/doi.org\/10.7287\/peerj.preprints.2843v1","relation":{},"subject":[],"published":{"date-parts":[[2017,3,2]]},"subtype":"preprint"}}