De novo transcriptome assembly with ABySS
De novo transcriptome assembly with ABySS
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DOI：
10.1093/bioinformatics/btp367
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发表时间：
2009-11-01
期刊：
影响因子：
5.8
通讯作者：
Jones, Steven J. M.
中科院分区：
文献类型：
--
作者：
Birol, Inanc;Jackman, Shaun D.;Jones, Steven J. M.
动机：来自非标准化样本的全转录组鸟枪测序数据为研究生物体的代谢状态提供了独特的机会。人们可以推断基因表达水平使用序列覆盖作为替代，识别编码变化或发现新的同工型或转录本。特别是对于新事件的发现，转录组的从头组装是可取的。结果：在Illumina Genome Analyzer II平台上，对1例滤泡性淋巴瘤患者肿瘤组织的转录组进行了36个碱基对（bp）的单端和成对端测序。我们使用ABySS将类似的1.94亿reads组装成66921个100 bp或更长的contigs，最大contigs长度为10951 bp，代表了超过3000万个碱基对的独特转录组序列，约占基因组的1%。
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.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 similar to 194 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.