Tools For Quality Trimming Of Solid Reads In Colorspace.

Question

[lin.barnum]

Are there any tools for quality filtering of solid reads in colorspace or is the best option to convert to csfastq, use something like seqtk and then convert back?

Answer 1

[Ashutosh Pandey]

Yup William is correct. Lifescope will trim the reads before it aligns. There is an option for that. If you want to use any other tool for alignment that doesnt do the trimming itself then you can use https://github.com/brentp/bio-playground/blob/master/solidstuff/solid-trimmer.py .

Answer 2

[Ian]

I just answered another question about this :) Maybe of use... Program for filtering SOLiD reads

There are also tools to help you do this on GALAXY. See the section "NGS: QC and manipulation".

Answer 3

[William]

Do you wan't to do the mapping with Lifescope or BWA? If you are using Lifescope, mabye there is an option in there to do the trimming. Lifescope supports clipping of the reads, by default it is enabled and it should remove a lot of the noisy tails of the reads.

Other than lifescope there are almost no tools that work directly with the SOLID native XSQ format. There are a couple of tools that convert XSQ to csFastq or csFasta. I also wrote one that support hard trimming of reads.

Once you have the data in csFasta or csFastq you could do the trimming if you find a tools that support the solid color space version of fastq and fasta. I am not sure if you then can convert back to XSQ, I think there is a tool from Life but I don't know if it works.