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?
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Allen Yu •
The Solid Accuracy Enhancer Tool might be useful for this.
edit: original link was pointing to a malware site.
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Curious George •
Thanks a lot for your kind help, the number of dots in csfasta reads does become lower.
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.
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Mikael Huss
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
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
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Istvan Albert
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