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Convert Illumina Solfastq To Fastq

Hi all,

I have single end sequencing data from an illumina GAII, the raw reads were returned to me in solfastq format however, the program i am currently trying to use will not accept this file type and requires a .fastq extension instead, does anyone know how i can convert solfatsq to fastq files? i am struggling to find a clear answer to this question ... Thanks for any help in advance!

illumina next-gen fastq
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updated by Peter Peter • written by saffi86 • saffi86

4 answers

BWA comes with a conversion script: solid2fastq.pl

MAQ also has some conversion scripts:

http://maq.sourceforge.net/maq-manpage.shtml

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written by Zev.Kronenberg Zev.Kronenberg

Hi, Check the comment no. 12 in this thread to get the script for conversion,if you like command line else try the galaxy's groomer tool for the conversion. More info here.

HTH

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written by Sukhi Singh Sukhi Singh

That's great, ill try those thanks for the quick response guys!

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written by saffi86 • saffi86

There are several tools listed on the wikipedia entry for FASTQ, http://en.wikipedia.org/wiki/FASTQ_format - of these seqret from the EMBOSS tool suite is a comprehensive sequence file format converter handling many other file formats too.

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written by Peter Peter

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