[Bioperl-l] Next-gen modules
cjfields at illinois.edu
Wed Jun 17 21:08:55 EDT 2009
On Jun 17, 2009, at 5:24 PM, Sendu Bala wrote:
> 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
>> > > 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.
>> 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).
That's (unfortunately) true. It may be easy to whip up something that
works, but it probably won't be fast.
>> 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.
Like this one?
I suppose if one were inclined, this could be wrapped with SWIG in
BioLib, but would it be worth it (maybe beyond grabbing the file
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