[Bioperl-l] Next-gen modules

George Hartzell 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?


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