Software to analyse mutations in sanger sequencing files

Question

[reilly.brian.m]

I am interested in finding a free software package to analyse sanger sequencing files (ab1).

The software needs to be able to align the sequences in the presence of indel mutations, as I am using this to validate CRISPR/Cas9 knockout of genes.

Currently I use the free version of Mutation Surveyor, but the free version cannot produce publication quality alignments as it has a watermark in the background of the alignment. I basically want a software that can perform largely the same function (alignment of sequences with indel mutations), that is open source/free/cheap.

Any recommendations would be great.

Thanks!

[Pappu]

Have you looked at UGENE?

Answer 1

[arno.guille]

I suggest you to use phred phrap consed

http://www.phrap.org/phredphrapconsed.html

Answer 2

[trausch]

Indigo analyses sanger sequencing files (ab1, abi, scf), separates het. InDel mutations and aligns the sequences to a reference genome, wildtype chromatogram or custom fasta file. It also works for homozygous mutations or SNP identification in general. Code is open-source and there is also a command-line backend called tracy.

Answer 3

[jawhar.saks]

Hello, I developped a workflow that does it automatically for whole batch and provide a conclusion suited to publications. Just mp me if you want to know about it.