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?
1 answer
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.
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It sounds like you're looking for SNPs - small differences between the reference genome and your read,s or I misunderstood your question.
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.
So tools for finding SNPs should be helpful here
How come you don't want to use samtools?