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