{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T07:03:17Z","timestamp":1773212597567,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Whole transcriptome shotgun sequencing data from non-normalized samples offer unique opportunities to study the metabolic states of organisms. One can deduce gene expression levels using sequence coverage as a surrogate, identify coding changes or discover novel isoforms or transcripts. Especially for discovery of novel events, de novo assembly of transcriptomes is desirable.<\/jats:p>\n               <jats:p>Results: Transcriptome from tumor tissue of a patient with follicular lymphoma was sequenced with 36 base pair (bp) single- and paired-end reads on the Illumina Genome Analyzer II platform. We assembled \u223c194 million reads using ABySS into 66 921 contigs 100 bp or longer, with a maximum contig length of 10 951 bp, representing over 30 million base pairs of unique transcriptome sequence, or roughly 1% of the genome.<\/jats:p>\n               <jats:p>Availability and Implementation: Source code and binaries of ABySS are freely available for download at http:\/\/www.bcgsc.ca\/platform\/bioinfo\/software\/abyss. Assembler tool is implemented in C++. The parallel version uses Open MPI. ABySS-Explorer tool is implemented in Java using the Java universal network\/graph framework.<\/jats:p>\n               <jats:p>Contact: \u00a0ibirol@bcgsc.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp367","type":"journal-article","created":{"date-parts":[[2009,6,16]],"date-time":"2009-06-16T00:26:03Z","timestamp":1245111963000},"page":"2872-2877","source":"Crossref","is-referenced-by-count":338,"title":["<i>De novo<\/i> transcriptome assembly with ABySS"],"prefix":"10.1093","volume":"25","author":[{"given":"Inan\u00e7","family":"Birol","sequence":"first","affiliation":[{"name":"1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada"}]},{"given":"Shaun D.","family":"Jackman","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada"}]},{"given":"Cydney B.","family":"Nielsen","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada"}]},{"given":"Jenny Q.","family":"Qian","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada"}]},{"given":"Richard","family":"Varhol","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada"}]},{"given":"Greg","family":"Stazyk","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada"}]},{"given":"Ryan D.","family":"Morin","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada"}]},{"given":"Yongjun","family":"Zhao","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada"}]},{"given":"Martin","family":"Hirst","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada"}]},{"given":"Jacqueline E.","family":"Schein","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada"}]},{"given":"Doug E.","family":"Horsman","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada"}]},{"given":"Joseph M.","family":"Connors","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada"}]},{"given":"Randy D.","family":"Gascoyne","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada"}]},{"given":"Marco A.","family":"Marra","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada"}]},{"given":"Steven J. M.","family":"Jones","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, 100-570 W 7th Avenue, Vancouver, BC V5Z 4S6 and 2 British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada"}]}],"member":"286","published-online":{"date-parts":[[2009,6,15]]},"reference":[{"key":"2023013112193705200_B1","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/nature07517","article-title":"Accurate whole human genome sequencing using reversible terminator chemistry","volume":"456","author":"Bentley","year":"2008","journal-title":"Nature"},{"key":"2023013112193705200_B2","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":"2023013112193705200_B3","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1101\/gr.7088808","article-title":"Short read fragment assembly of bacterial genomes","volume":"18","author":"Chaisson","year":"2008","journal-title":"Genome Res."},{"key":"2023013112193705200_B4","first-page":"758","article-title":"A combinatorial problem","volume":"49","author":"de Bruijn","year":"1946","journal-title":"Koninklijke Nederlandse Akademie v. Wetenschappen"},{"key":"2023013112193705200_B5","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":"11","author":"Dohm","year":"2007","journal-title":"Genome Res."},{"key":"2023013112193705200_B6","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1111\/j.1574-6968.2008.01441.x","article-title":"De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina\/Solexa short sequence reads","volume":"1","author":"Farrer","year":"2009","journal-title":"FEMS Microbiol. Lett."},{"key":"2023013112193705200_B7","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1101\/gr.074906.107","article-title":"Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses","volume":"4","author":"Fullwood","year":"2009","journal-title":"Genome Res."},{"key":"2023013112193705200_B8","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1101\/gr.072033.107","article-title":"De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer","volume":"5","author":"Hernandez","year":"2008","journal-title":"Genome Res."},{"key":"2023013112193705200_B9","doi-asserted-by":"crossref","first-page":"1036","DOI":"10.1093\/bioinformatics\/btl048","article-title":"The UCSC known genes","volume":"9","author":"Hsu","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013112193705200_B10","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1186\/1471-2105-10-S1-S14","article-title":"Parallel short sequence assembly of transcriptomes","volume":"10","author":"Jackson","year":"2009","journal-title":"BMC Bioinform."},{"key":"2023013112193705200_B11","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi0104s17","article-title":"The UCSC Genome Browser","author":"Karolchik","year":"2007","journal-title":"Curr. Protoc. Bioinform."},{"key":"2023013112193705200_B12","first-page":"656","article-title":"BLAT \u2013 the BLAST-like alignment tool","volume":"4","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023013112193705200_B13","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/nmeth.1311","article-title":"Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes","volume":"4","author":"Kozarewa","year":"2009","journal-title":"Nat. Methods"},{"key":"2023013112193705200_B14","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1101\/gr.078212.108","article-title":"Mapping short DNA sequencing reads and calling variants using mapping quality scores","volume":"11","author":"Li","year":"2008","journal-title":"Genome Res."},{"key":"2023013112193705200_B15","doi-asserted-by":"crossref","first-page":"81","DOI":"10.2144\/000112900","article-title":"Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing","volume":"45","author":"Morin","year":"2008","journal-title":"Biotechniques"},{"key":"2023013112193705200_B16","doi-asserted-by":"crossref","DOI":"10.1109\/TVCG.2009.116","article-title":"ABySS-Explorer: visualizing genome sequence assemblies","author":"Nielsen","year":"2009","journal-title":"IEEE Trans. Vis. Comp. Graphics (in revision)."},{"key":"2023013112193705200_B17","doi-asserted-by":"crossref","first-page":"2024","DOI":"10.1101\/gr.080200.108","article-title":"Sequencing of natural strains of Arabidopsis thaliana with short reads","volume":"12","author":"Ossowski","year":"2008","journal-title":"Genome Res."},{"key":"2023013112193705200_B18","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. Natl Acad. Sci. USA"},{"key":"2023013112193705200_B19","doi-asserted-by":"crossref","first-page":"e1000186","DOI":"10.1371\/journal.pcbi.1000186","article-title":"Gene-boosted assembly of a novel bacterial genome from very short reads","volume":"9","author":"Salzberg","year":"2008","journal-title":"PLoS Comput Biol."},{"key":"2023013112193705200_B20","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1101\/gr.089532.108","article-title":"ABySS: a parallel assembler for short read sequence data","volume":"19","author":"Simpson","year":"2009","journal-title":"Genome Res."},{"key":"2023013112193705200_B21","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/1471-2105-6-31","article-title":"Automated generation of heuristics for biological sequence comparison","volume":"6","author":"Slater","year":"2005","journal-title":"BMC Bioinform."},{"key":"2023013112193705200_B22","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/nature07509","article-title":"Alternative isoform regulation in human tissue transcriptomes","volume":"456","author":"Wang","year":"2008","journal-title":"Nature"},{"key":"2023013112193705200_B23","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1093\/bioinformatics\/btp010","article-title":"Profiling model T-cell metagenomes with short reads","volume":"4","author":"Warren","year":"2009","journal-title":"Bioinformatics"},{"key":"2023013112193705200_B24","doi-asserted-by":"crossref","first-page":"3264","DOI":"10.1073\/pnas.0812841106","article-title":"Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing","volume":"9","author":"Yassour","year":"2009","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013112193705200_B25","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for de novo short read assembly using de Bruijn graphs","volume":"18","author":"Zerbino","year":"2008","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/21\/2872\/48998145\/bioinformatics_25_21_2872.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/21\/2872\/48998145\/bioinformatics_25_21_2872.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:59:28Z","timestamp":1675202368000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/21\/2872\/2111463"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,6,15]]},"references-count":25,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2009,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp367","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,11,1]]},"published":{"date-parts":[[2009,6,15]]}}}