Gap Alignment For Color Space Data (Blat For Color Space!)

Question

[seqseek]

Hi All,

Is there a way to do gap alignment on ABI SOLiD color space data? I could convert color space into base space and use BLAT, but I'm sure that there is a better way to do it.

Thanks!

[Michael Kuhn]

sorry, what exactly do you want to do? Do you mean RGB / HSL color space? Can you show an example?

[Michael]

I think ABI Solid sequencing data in "color space" is meant here.

Answer 1

[Michael]

Have a look at this ever growing list

According to its description BFAST could do it. Haven't used it myself but read some promising comments. From the wiki page:

Can handle insertions, deletions, SNPs, and color errors (can map ABI SOLiD color space reads). Performs a full Smith Waterman alignment.

[User 59]

Having looked into this issue a few weeks ago, I think BFAST was the only tool I found that claimed to be able to do this.

[Istvan Albert]

SHRiMP, (see below) was probably the first aligner designed for colorspace

Answer 2

[Jonathan Manning]

In addition to BFAST, which has excellent support for colorspace reads and produces gapped alignments, the AB SOLiD Bioscope software supports gapped alignments via the small indel tool.

Direct conversion of color space reads into dna-space will result in very high error rates and is not recommended.

Answer 3

[Istvan Albert]

SHRiMP was designed primarily for colorspace data. Once it finds likely locations it will do a full alignment.

The main publication describes the method in detail.