Question: Gap Alignment For Color Space Data (Blat For Color Space!)
2
gravatar for seqseek
9.3 years ago by
seqseek20
seqseek20 wrote:

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!

short aligner solid blat • 2.6k views
ADD COMMENTlink modified 9.3 years ago by Istvan Albert ♦♦ 81k • written 9.3 years ago by seqseek20

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

ADD REPLYlink written 9.3 years ago by Michael Kuhn5.0k

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

ADD REPLYlink written 9.3 years ago by Michael Dondrup46k
3
gravatar for Michael Dondrup
9.3 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

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.

ADD COMMENTlink modified 11 months ago by RamRS23k • written 9.3 years ago by Michael Dondrup46k

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.

ADD REPLYlink written 9.3 years ago by Daniel Swan13k

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

ADD REPLYlink written 9.3 years ago by Istvan Albert ♦♦ 81k
1
gravatar for Jonathan Manning
9.3 years ago by
Near Boston, MA
Jonathan Manning630 wrote:

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.

ADD COMMENTlink written 9.3 years ago by Jonathan Manning630
1
gravatar for Istvan Albert
9.3 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

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.

ADD COMMENTlink written 9.3 years ago by Istvan Albert ♦♦ 81k
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