Program For Filtering Solid Reads
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8.6 years ago
lin.barnum ▴ 230

A filtering program for filtering SOLiD reads directly without converting to fastq was described in http://bioinformatics.oxfordjournals.org/content/26/6/849.short?rss=1 and should have been available at http://hts.rutgers.edu/filter

Unfortunately, that website is closed. Would anyone have a copy of the program?

solid ngs quality • 2.6k views
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Well there are many other scripts available that will do the same job. Some of them are even faster than what you are talking about. If I remember it correctly they wrote a perl code. Search for filtering SOLID reads in the forum and you will get many posts about it.

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8.6 years ago
Ian 5.8k

Here is the Perl script: https://github.com/fls-bioinformatics-core/HTS_SOLiD_Preprocessing [moved from my old Dropbox folder 20 Oct. 2015]

We still use this script to prefilter SOLiD sequencing runs.

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8.6 years ago
brentp 23k

I wrote this: https://github.com/brentp/bio-playground/blob/master/solidstuff/solid-trimmer.py

which can trim a .csasta + .qual file and output the format of your choosing (BWA/BFAST or csfasta and qual)

If you're talking about their hdf5 formatted data, I don't know of a tool to trim directly from that without exporting first.

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