looking for reference genome based assembler for short-reads

[zchou]

Hi All,

I want to use comparative-based assembler for short-reads for assembling mRNA-seq. For example, if we have human tissue mRNA short-reads, we want to reassemble the short-reads into transcripts by comparing with human genome, which software is more suitable for this task?

I found AMOScmp-shortreads might be useful for this purpose, but when I read the manual, I found AMOScmp do not support fastq format. I also don't know the performance for this software.

In further, do anyone compare the performance of de novo based assembler with reference-based assembler for mRNA-seq?

Thanks,
ZCH

[krobison]

The RNA-Seq section of the software wiki at this site has 14 entries; not all of them perform mapping but you should find several tools there which might be candidates for your needs.

http://seqanswers.com/wiki/Special:BrowseData/Bioinformatics%20application?Biological_domain=RNA-Seq

[zchou]

As the lists of this webpage "Software packages for next gen sequence analysis" includes many different tools for mapping/assembling. However, no any software designed for this purpose. MAQ has limited function to generate the consensus sequences based on mapping. However, it seems MAQ can only use reads length lower than 63bp. As I listed, AMOScmp-short-reads is only software I know to provide this function, but weak support for paired-end illumina GAII sequences files(qseq) or fastq.

[Xi Wang]

Check Tophat and Cufflink.