How To Do Quality Trimming Of Solid Reads In Colour Space?
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11.7 years ago
Allen Yu ▴ 200

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?

solid • 4.8k views
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11.7 years ago

The Solid Accuracy Enhancer Tool might be useful for this.

edit: original link was pointing to a malware site.

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

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11.6 years ago

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

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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7.1 years ago

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

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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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