Is There A Way To Start From 454'S ".Fna" And ".Qual" Files In Gkno?

Question

[Carlos Borroto]

Hi,

I guess my question is, is there a tool already integrated into gkno to merge 454's ".fna" and ".qual" files into a FASTQ file? If not, any recommendation on a good candidate tool for which I could write the JSON configuration?

Thanks, Carlos

Answer 1

[Istvan Albert]

There are a few post discussing converting 454 fasta/qual into FASTQ:

convert fas/qual into fastq?

and

How to convert 454 data to SAM format?

[Carlos Borroto]

You are correct, I could always use some script(I actually wrote my own using Biopython) to do this work before running gkno, but that would defeat the purpose of doing everything inside a very convenient gkno pipeline. And to the second part of my question, if gkno doesn't have such a tool currently, I would like to hear comments on a mature tool that could get integrated into gkno to do the conversion. There is some work involve in integrating a tool into gkno, I would like to do such work for a mature tool if there is one.

Thanks, Carlos