Fastq groomer from command line

[Giles]

Does anyone know of a script that allows one to convert Qual scores from a fastq file in order to map w/ BWA or Bowtie using the command line? I'm familar with the Galaxy tools function, but Galaxy has really been unreliable lately, I'd love to move away from it whenever possible.

[nilshomer]

I may be confused by your question, but BWA/bowtie take fastq files as input.

[Giles]

The qual portion of fastq comes in different varieties. Bwa and bowtie only accept one format. The galaxy fastq groomer changes the qual score format to allow bwa or bowtie compatibility. I would like to run that script from the command line, and I wondered if anyone knew where to find it.

[kmcarr]

The qual portion of fastq comes in different varieties. Bwa and bowtie only accept one format...

Not true. Both bwa and bowtie can use directly FASTQ files with Q-scores encoded as either Phred+33 (Sanger standard) or Phred+64 (Illumina prior to CASAVA 1.8). You just need to set the proper option on the command line.

bowtie: --phred-33 (default) or --phred-64

bwa aln: (default is Phred+33, no option required) or -I (Phred+64).

Check the manuals for both of these programs for specifics.

[maubp]

There are several other options for doing the conversion if you need to, e.g. EMBOSS seqret
http://dx.doi.org/10.1093/nar/gkp1137