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De novo assembly and analysis of RNA-seq data

Robertson, Gordon; Schein, Jacqueline E; Chiu, Readman; Corbett, Richard; Field, Matthew; Jackman, Shaun D.; Mungall, Karen; Lee, Sam; Okada, Hisanaga Mark; Qian, Jenny Q; Griffith, Malachi; Raymond, Anthony; Thiessen, Nona; Cezard, Timothee


We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads from an adult mouse liver poly(A) RNA library, we identified known, new and alternative structures in expressed transcripts, and achieved high sensitivity and specificity relative...[Show more]

CollectionsANU Research Publications
Date published: 2010
Type: Journal article
Source: Nature Methods: techniques for life scientists and chemists
DOI: 10.1038/nmeth.1517


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