Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
Nat Methods. 2010 Nov;7(11):909-12. doi: 10.1038/nmeth.1517. Epub 2010 Oct 10.
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 to reference-based assembly methods.
我们描述了 Trans-ABySS，这是一种从头开始的短读长转录组组装和分析管道，通过使用不同严格程度的读子序列进行组装，然后在分析前合并得到的 contigs，从而解决局部读密度变化的问题。我们分析了来自成年小鼠肝 poly(A) RNA 文库的 74 亿碱基对 50 碱基对的双端 Illumina 读长，鉴定了已知的、新的和替代的表达转录本结构，并与基于参考的组装方法相比，实现了高灵敏度和特异性。
