Convert Illumina Solfastq To Fastq

Question

[saffi86]

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!

Answer 1

[Zev.Kronenberg]

BWA comes with a conversion script: solid2fastq.pl

MAQ also has some conversion scripts:

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

Answer 2

[Sukhi Singh]

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

Answer 3

[saffi86]

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

Answer 4

[Peter]

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.