How To Do Quality Trimming Of Solid Reads In Colour Space?

Question

[Allen Yu]

The reads returned from the Solid sequencing provider are littered with dots and some bases have a negative quality value. Does anyone know if there is a good method to extract high quality regions from the reads without distorting the reading of bases in colour space?

Answer 1

[Curious George]

The Solid Accuracy Enhancer Tool might be useful for this.

edit: original link was pointing to a malware site.

[Allen Yu]

Thanks a lot for your kind help, the number of dots in csfasta reads does become lower.

Answer 2

[Mikael Huss]

I know of two quality filtering methods for SOLiD reads, besides the already suggested SAET:

• A set of tools from a recent publication

• The csfastaqualityfilter.pl script from ABI's de novo accessory tools package

Haven't actually tried any of them yet, but will do so pretty soon.

edit: original link to the csfastaqualityfilter.pl was pointing to a malware site.

Answer 3

[Antonio R. Franco]

It seems that the Dr. Michael's tool are not longer available, neither the csfastaqualityfilter.pl

Can anyboy either send me these tools/scripts to me or indicate where to get them? My address is arfranco (at) uco.es

[Istvan Albert]

There are some tools still available on our site, see if SAET would work for you:

Solid Software Tools: Denovo Assembly/Xsq Tools Pipeline Mirrored At Biostar