Question: Software to analyse mutations in sanger sequencing files
gravatar for reilly.brian.m
5.0 years ago by
United States
reilly.brian.m60 wrote:

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.


ADD COMMENTlink modified 2.4 years ago by trausch1.5k • written 5.0 years ago by reilly.brian.m60

Have you looked at UGENE?

ADD REPLYlink written 5.0 years ago by Pappu1.9k
gravatar for arno.guille
5.0 years ago by
arno.guille400 wrote:

I suggest you to use phred phrap consed

ADD COMMENTlink written 5.0 years ago by arno.guille400
gravatar for trausch
2.4 years ago by
trausch1.5k wrote:

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.

ADD COMMENTlink modified 8 months ago • written 2.4 years ago by trausch1.5k
gravatar for jawhar.saks
2.5 years ago by
jawhar.saks10 wrote:

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.

ADD COMMENTlink written 2.5 years ago by jawhar.saks10
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