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De novo RNA Assembly AND RNA Resequencing  

2011-07-23 08:17:23|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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Sequencing mRNA of species without a reference genome. The followings are software developed for de novo assembly short reads coming from RNA-seq.


Velvet+Oases
Velvet+Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of reference genome.
ABySS


RNA Resequencing

Resequencing and mapping mRNA of species with a reference genome (e.g. Human). The followings are software developed for mapping reads, detecting splicing isoforms, and estimating expression level of RNA-seq.


TopHat
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
Cufflink
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.
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