[Bioperl-l] Next-gen modules
bix at sendu.me.uk
Wed Jun 17 18:24:50 EDT 2009
George Hartzell wrote:
> 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?
Too heavy-weight, too slow, too memory intensive, missing too much
functionality in any case. If I have to write new parsers and wrappers,
I may as well make them fast (which means they don't "fit" into BioPerl).
> What *are* you using?
There are already great tools written in C that do all the heavy lifting
and the rest is done in perl written for speed and low memory.
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