Improving Transcriptome Sequence With Illumina Reads

Question

[xmix]

Hello Biostars,

I wonder whether there are tools that take an existing genome / transcriptome assembly (fasta), and correct it with short-sequences data (or with SAM/BAM files from that kind of data). Even a tool that will correct mismatches and short indels will be of use by consensus calling. I downloaded iCorn, but read that it requires mate-pair data, which I do not have. Are there alternatives to a samtools / vcf2fq combination?

[Asaf]

It sounds like you're looking for SNPs - small differences between the reference genome and your read,s or I misunderstood your question.

[xmix]

Most of them are not true SNPs but errors that are the result of imperfect assembly. The most annoying errors are "frame-shifts" due to error in the assembly of homopolymers.

[Asaf]

So tools for finding SNPs should be helpful here

[Dan]

How come you don't want to use samtools?

Answer 1

[SES]

You may want to try SEQuel which does not require mate pair information (see the publication for more details) but it does require a fasta reference, not SAM/BAM. I came across this tool recently and haven't had a chance to try it, so I'd be interested in the results.