{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T17:35:23Z","timestamp":1772645723872,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2018,11,10]],"date-time":"2018-11-10T00:00:00Z","timestamp":1541808000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/N016742\/1"],"award-info":[{"award-number":["BB\/N016742\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/N01720X\/1"],"award-info":[{"award-number":["BB\/N01720X\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"BBSRC","doi-asserted-by":"publisher","award":["BB\/P013759\/1"],"award-info":[{"award-number":["BB\/P013759\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"BBSRC","doi-asserted-by":"publisher","award":["BB\/P013732\/1"],"award-info":[{"award-number":["BB\/P013732\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"BBSRC","doi-asserted-by":"publisher","award":["BB\/J004235\/1"],"award-info":[{"award-number":["BB\/J004235\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"BBSRC","doi-asserted-by":"publisher","award":["BB\/J004243\/1"],"award-info":[{"award-number":["BB\/J004243\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012095","name":"Scottish Government","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100012095","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Metagenomics is a powerful tool for assaying the DNA from every genome present in an environment. Recent advances in bioinformatics have enabled the rapid assembly of near-complete metagenome-assembled genomes (MAGs), and there is a need for reproducible pipelines that can annotate and characterize thousands of genomes simultaneously, to enable identification and functional characterization.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here we present MAGpy, a scalable and reproducible pipeline that takes multiple genome assemblies as FASTA and compares them to several public databases, checks quality, suggests a taxonomy and draws a phylogenetic tree.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>MAGpy is available on github: https:\/\/github.com\/WatsonLab\/MAGpy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty905","type":"journal-article","created":{"date-parts":[[2018,11,10]],"date-time":"2018-11-10T00:43:22Z","timestamp":1541810602000},"page":"2150-2152","source":"Crossref","is-referenced-by-count":33,"title":["MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs)"],"prefix":"10.1093","volume":"35","author":[{"given":"Robert D","family":"Stewart","sequence":"first","affiliation":[{"name":"The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, UK"}]},{"given":"Marc D","family":"Auffret","sequence":"additional","affiliation":[{"name":"Scotland\u2019s Rural College, Easter Bush, UK"}]},{"given":"Timothy J","family":"Snelling","sequence":"additional","affiliation":[{"name":"The Rowett Institute of Nutrition and Health, University of Aberdeen, King\u2019s College, Aberdeen, UK"}]},{"given":"Rainer","family":"Roehe","sequence":"additional","affiliation":[{"name":"Scotland\u2019s Rural College, Easter Bush, UK"}]},{"given":"Mick","family":"Watson","sequence":"additional","affiliation":[{"name":"The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, UK"}]}],"member":"286","published-online":{"date-parts":[[2018,11,10]]},"reference":[{"key":"2023012713225981600_bty905-B1","doi-asserted-by":"crossref","first-page":"e1029","DOI":"10.7717\/peerj.1029","article-title":"Compact graphical representation of phylogenetic data and metadata with GraPhlAn","volume":"3","author":"Asnicar","year":"2015","journal-title":"PeerJ"},{"key":"2023012713225981600_bty905-B2","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST Server: rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"2023012713225981600_bty905-B3","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/nbt.3893","article-title":"Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea","volume":"35","author":"Bowers","year":"2017","journal-title":"Nat. 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