SHRiMP and SOLiD Qualities

[agc]

I want to run SHRiMP on SOLiD data, but despite reading the manual I can't find a parameter that allows me to give the .qual file as input. Does SHRiMP not consider quality values at all?

[pmiguel]

I want to run SHRiMP on SOLiD data, but despite reading the manual I can't find a parameter that allows me to give the .qual file as input. Does SHRiMP not consider quality values at all?

Probably not. Shrimp is a tool from the corona-lite days. Back then the qual values were pretty much ignored by most tools. I think it was not until BioScope that qual values started being used in ABI's pipeline.

--
Phillip

[agc]

A new version of SHRiMP was released just last month, so it can't be that outdated. And I think I saw somewhere that it does take quality values into consideration.

[pmiguel]

A new version of SHRiMP was released just last month, so it can't be that outdated. And I think I saw somewhere that it does take quality values into consideration.

Yes, perhaps http://compbio.cs.toronto.edu/shrimp/HISTORY:

2.0.2: Sep 20, 2010
[...]
- Added --bfast option that performs global color space alignments
along with reporting color space base qualities

But this does not indicate that quality values are used in mapping, only that with the --bfast option that "color space base qualities" are reported.

--
Phillip

[brudno]

SHRiMP for now only reports the qualities (per-color, and also per-base in the exact same way as bfast). They are not (yet) used for actual mapping, though that is very high on our agenda.

-Mike

[apredeus]

It's still the case, isn't it? The qualities for individual bases are not used in actual alignment?

[mateidavid]

SHRiMP has been using mapping quality values since v2.2.0 in August 2011. If the reads are given in .fasta files, all colors use a default qv corresponding to 3% error rate (about 17). If they are given in fastq files, the qualities are interpreted according to the PHRED value and used as integral part of the alignment. It doesn't take .qual input directly. See such options as --pr-xover, --min-avg-qv, --qv-offset, --ignore-qvs in README.