Assembly For Rare Variants

Question

[Biomed]

If you detect a very rare variant using short reads (illumina) there is a good chance that it can be a sequencing error as well. Let's say I want to do some local assembly to get a better result in variant detection at this region around the detected variant. First of all, do you think this is a good idea? If so, given that there are many assemblers out there, which one do you suggest should be used for this purpose, manly based on the quality of results and ease of use for this purpose.

Thank you

[Istvan Albert]

Frankly when it comes to very rare variants there are no easy to use tools. You really need to make sure to understand the entire process, to be able to make a credible statement.

[Biomed]

I agree with you but can you be a little more specific?

[Istvan Albert]

The problem that you describe is quite challenging even when mapping against a known genome: http://www.broadinstitute.org/gsa/wiki/index.php/MPG_Next-Generation_DNA_sequencing_tutorials, I imagine that trying to do the same while assembling a new sequence must be even more complicated.

Answer 1

[Lee Katz]

Nesoni is a pretty good multipurpose tool that uses shrimp and samtools.

[Biomed]

thanks, looks promising