{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,4,11]],"date-time":"2024-04-11T23:28:51Z","timestamp":1712878131369},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Many de novo genome assemblers have been proposed recently. The basis for most existing methods relies on the de bruijn graph: a complex graph structure that attempts to encompass the entire genome. Such graphs can be prohibitively large, may fail to capture subtle information and is difficult to be parallelized.<\/jats:p>\n               <jats:p>Result: We present a method that eschews the traditional graph-based approach in favor of a simple 3\u2032 extension approach that has potential to be massively parallelized. Our results show that it is able to obtain assemblies that are more contiguous, complete and less error prone compared with existing methods.<\/jats:p>\n               <jats:p>Availability: The software package can be found at http:\/\/www.comp.nus.edu.sg\/~bioinfo\/peasm\/. Alternatively it is available from authors upon request.<\/jats:p>\n               <jats:p>Contact: \u00a0ksung@comp.nus.edu.sg; sungk@gis.a-star.edu.sg<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq626","type":"journal-article","created":{"date-parts":[[2010,12,14]],"date-time":"2010-12-14T04:21:31Z","timestamp":1292300491000},"page":"167-174","source":"Crossref","is-referenced-by-count":40,"title":["PE-Assembler: <i>de novo<\/i> assembler using short paired-end reads"],"prefix":"10.1093","volume":"27","author":[{"given":"Pramila Nuwantha","family":"Ariyaratne","sequence":"first","affiliation":[{"name":"1 Computational & Mathematical Biology Group, Genome Institute of Singapore, 138672 and 2School of Computing, National University of Singapore, Singapore 117543"}]},{"given":"Wing-Kin","family":"Sung","sequence":"additional","affiliation":[{"name":"1 Computational & Mathematical Biology Group, Genome Institute of Singapore, 138672 and 2School of Computing, National University of Singapore, Singapore 117543"},{"name":"1 Computational & Mathematical Biology Group, Genome Institute of Singapore, 138672 and 2School of Computing, National University of Singapore, Singapore 117543"}]}],"member":"286","published-online":{"date-parts":[[2010,12,12]]},"reference":[{"key":"2023012512175678000_B1","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1101\/gr.7337908","article-title":"ALLPATHS: de novo assembly of whole-genome shotgun microreads","volume":"18","author":"Butler","year":"2008","journal-title":"Genome Res."},{"key":"2023012512175678000_B2","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1101\/gr.079053.108","article-title":"De novo fragment assembly with short mate-paired reads: Does the read length matter?","volume":"19","author":"Chaisson","year":"2009","journal-title":"Genome Res."},{"key":"2023012512175678000_B3","doi-asserted-by":"crossref","first-page":"1697","DOI":"10.1101\/gr.6435207","article-title":"SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing","volume":"17","author":"Dohm","year":"2007","journal-title":"Genome Res."},{"key":"2023012512175678000_B4","doi-asserted-by":"crossref","first-page":"2942","DOI":"10.1093\/bioinformatics\/btm451","article-title":"Extending assembly of short DNA sequences to handle error","volume":"23","author":"Jeck","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012512175678000_B5","first-page":"656","article-title":"BLAT\u2013the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023012512175678000_B6","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1101\/gr.097261.109","article-title":"De novo assembly of human genomes with massively parallel short read sequencing","volume":"20","author":"Li","year":"2010","journal-title":"Genome Res."},{"key":"2023012512175678000_B7","doi-asserted-by":"crossref","first-page":"R103","DOI":"10.1186\/gb-2009-10-10-r103","article-title":"ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads","volume":"10","author":"MacCallum","year":"2009","journal-title":"Genome Biol."},{"key":"2023012512175678000_B8","doi-asserted-by":"crossref","first-page":"9748","DOI":"10.1073\/pnas.171285098","article-title":"An Eulerian path approach to DNA fragment assembly","volume":"98","author":"Pevzner","year":"2001","journal-title":"Proc. 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