Program For Filtering Solid Reads

Question

[lin.barnum]

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?

[Ashutosh Pandey]

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.

Answer 1

[Ian]

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.

Answer 2

[brentp]

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.