[Bioperl-l] Next-gen modules
hartzell at alerce.com
Wed Jun 17 16:40:03 EDT 2009
Sendu Bala writes:
> Tristan Lefebure wrote:
> > Hello,
> > Regarding next-gen sequences and bioperl, following my
> > experience, another issue is bioperl speed. For example, if
> > you want to trim bad quality bases at ends of 1E6 Solexa
> > reads using Bio::SeqIO::fastq and some methods in
> > Bio::Seq::Quality, well, you've got to be patient (but may
> > be I missed some shortcuts...).
> This is my concern as well. Or, rather, is there actually a significant
> set of users out there who are dealing with next-gen sequencing and
> would consider using BioPerl for their work?
> I'm working with all the 1000-genomes data at the Sanger, and we at
> least are probably never going to use BioPerl for the work.
Is it purely a speed issue, or are there other issues (e.g. stability,
correctness, compatibility) that are contributing to your decision?
What *are* you using?
More information about the Bioperl-l