{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T03:35:13Z","timestamp":1776483313401,"version":"3.51.2"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1682,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: High-throughput sequencing has made the analysis of new model organisms more affordable. Although assembling a new genome can still be costly and difficult, it is possible to use RNA-seq to sequence mRNA. In the absence of a known genome, it is necessary to assemble these sequences de novo, taking into account possible alternative isoforms and the dynamic range of expression values.<\/jats:p><jats:p>Results: We present a software package named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms. It achieves this by using an array of hash lengths, a dynamic filtering of noise, a robust resolution of alternative splicing events and the efficient merging of multiple assemblies. It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers.<\/jats:p><jats:p>Availability and implementation: Oases is freely available under the GPL license at www.ebi.ac.uk\/~zerbino\/oases\/<\/jats:p><jats:p>Contact: \u00a0dzerbino@ucsc.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts094","type":"journal-article","created":{"date-parts":[[2012,2,25]],"date-time":"2012-02-25T03:45:12Z","timestamp":1330141512000},"page":"1086-1092","source":"Crossref","is-referenced-by-count":1271,"title":["<i>Oases:<\/i>robust<i>de novo<\/i>RNA-seq assembly across the dynamic range of expression levels"],"prefix":"10.1093","volume":"28","author":[{"given":"Marcel H.","family":"Schulz","sequence":"first","affiliation":[]},{"given":"Daniel R.","family":"Zerbino","sequence":"additional","affiliation":[]},{"given":"Martin","family":"Vingron","sequence":"additional","affiliation":[]},{"given":"Ewan","family":"Birney","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2012,2,24]]},"reference":[{"key":"2023012711533984500_B1","doi-asserted-by":"crossref","first-page":"2872","DOI":"10.1093\/bioinformatics\/btp367","article-title":"De novo transcriptome assembly with ABySS","volume":"25","author":"Birol","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012711533984500_B2","doi-asserted-by":"crossref","first-page":"1379","DOI":"10.1101\/gad.1788009","article-title":"Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes","volume":"23","author":"Blencowe","year":"2009","journal-title":"Gene. 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