{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T05:40:29Z","timestamp":1786426829303,"version":"3.56.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,2,15]]},"abstract":"<jats:p>Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina data.<\/jats:p>\n               <jats:p>Results: A5-miseq can produce high-quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation and includes several improvements to read trimming. Together, these changes result in substantially improved assemblies that recover a more complete set of reference genes than previous methods.<\/jats:p>\n               <jats:p>Availability: A5-miseq is licensed under the GPL open-source license. Source code and precompiled binaries for Mac OS X 10.6+ and Linux 2.6.15+ are available from http:\/\/sourceforge.net\/projects\/ngopt<\/jats:p>\n               <jats:p>Contact: aaron.darling@uts.edu.au<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu661","type":"journal-article","created":{"date-parts":[[2014,10,23]],"date-time":"2014-10-23T00:08:46Z","timestamp":1414022926000},"page":"587-589","source":"Crossref","is-referenced-by-count":1052,"title":["A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data"],"prefix":"10.1093","volume":"31","author":[{"given":"David","family":"Coil","sequence":"first","affiliation":[{"name":"1 \u00a01Genome Center, University of California Davis, Davis, CA 95616, USA and 2ithree institute, University of Technology Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guillaume","family":"Jospin","sequence":"additional","affiliation":[{"name":"1 \u00a01Genome Center, University of California Davis, Davis, CA 95616, USA and 2ithree institute, University of Technology Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aaron E.","family":"Darling","sequence":"additional","affiliation":[{"name":"1 \u00a01Genome Center, University of California Davis, Davis, CA 95616, USA and 2ithree institute, University of Technology Sydney, New South Wales, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,10,22]]},"reference":[{"key":"2023020108564231600_btu661-B1","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"2023020108564231600_btu661-B2","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020108564231600_btu661-B3","doi-asserted-by":"crossref","first-page":"W622","DOI":"10.1093\/nar\/gks540","article-title":"RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics","volume":"40","author":"Lohse","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023020108564231600_btu661-B4","doi-asserted-by":"crossref","first-page":"1718","DOI":"10.1093\/bioinformatics\/btt273","article-title":"GAGE-B: an evaluation of genome assemblers for bacterial organisms","volume":"29","author":"Magoc","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020108564231600_btu661-B5","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1093\/bioinformatics\/bts174","article-title":"IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth","volume":"28","author":"Peng","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020108564231600_btu661-B6","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1101\/gr.126953.111","article-title":"Efficient de novo assembly of large genomes using compressed data structures","volume":"22","author":"Simpson","year":"2012","journal-title":"Genome Res."},{"key":"2023020108564231600_btu661-B7","doi-asserted-by":"crossref","first-page":"e42304","DOI":"10.1371\/journal.pone.0042304","article-title":"An integrated pipeline for de novo assembly of microbial genomes","volume":"7","author":"Tritt","year":"2012","journal-title":"PLoS One"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/4\/587\/49011019\/bioinformatics_31_4_587.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/4\/587\/49011019\/bioinformatics_31_4_587.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T18:44:31Z","timestamp":1675277071000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/4\/587\/2748163"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,10,22]]},"references-count":7,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2015,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu661","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,10,22]]}}}