Question: Improving Transcriptome Sequence With Illumina Reads
0
gravatar for xmix
6.1 years ago by
xmix40
United States
xmix40 wrote:

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?

vcf consensus • 1.2k views
ADD COMMENTlink modified 6.1 years ago by SES8.1k • written 6.1 years ago by xmix40

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

ADD REPLYlink written 6.1 years ago by Asaf5.3k

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.

ADD REPLYlink written 6.1 years ago by xmix40

So tools for finding SNPs should be helpful here

ADD REPLYlink written 6.1 years ago by Asaf5.3k

How come you don't want to use samtools?

ADD REPLYlink written 6.1 years ago by Dan500
1
gravatar for SES
6.1 years ago by
SES8.1k
Vancouver, BC
SES8.1k wrote:

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.

ADD COMMENTlink written 6.1 years ago by SES8.1k
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