Software genome align and mutation finder

[fefe89]

Hi, I have 2 bacterial genomes (wt and mut) sequenced.

I've already assembled the genomes with velvet and mauve.

What I need now is a software that let me to align them and easily (and possibly with a graphical interface, since then It should also be used by non-bioinformatician) identify the presence of point mutation, deletions and insertions.


Any ideas?

[fefe89]

Is there anyone that can help me??

[Brian Bushnell]

If you want to identify mutations, you can map the reads of the mutant to the wild-type assembly and call variants with a variant caller. For example, with the BBMap package:

bbmap.sh in=mut_reads.fq ref=wt_assembly.fasta out=mapped.sam bs=bs.sh

callvariants.sh in=mapped.sam ref=wt_assembly.fasta vcf=variants.vcf

Then the variants are in the variants.vcf file, which is fairly easy to read. You can look at the variants visually in a program like IGV using the sorted, indexed bam file, which can be produced by running the shell script bs.sh that gets created by BBMap.

[fefe89]

Thaks a lot. I'll try this way