On Wed, Dec 15, 2010 at 2:42 AM, Florent Angly <florent.angly@gmail.com> wrote:
Hi,
I was wondering if there is a tool in Galaxy to put mate pair reads located in two files inside a single file? I made the error of believing that the FASTQ joiner does that, but it does not.
If this feature is not planned, I am willing to work on it. Which of the following would be better for integration into Galaxy? * a clean Python implementation like the other utilities in tools/fastq/, i.e. fastq_groomer.py and fastq_paired_end_joiner.py * a wrapper around the Velvet utilities, shuffleSequences_fastq.pl and shuffleSequences_fasta.pl, given that Velvet already has a wrapper in Galaxy
Are you asking for a tool to interleave to FASTQ or FASTA files with matching entries (with matching names in the same order) into one file which alternates forward then reverse read? Would you prefer it with or without error checking? I think the scripts in velvet are fast but will fail horribly with bad input... note there is a simple Biopython script to do this included with velvet already (simple version with no error checking, I have written a more robust version too - it looks like I haven't sent it to Daniel to include in velvet though). Peter