[Bioperl-l] please recommend a book about next-generation sequencer -> bioperl

[Alexey Morozov]

Also I think Bioperl and Perl in general is not the language of choice for
work with raw sequencer data. You probably will want to either assemble it,
align it to some refernece genome or measure metagenomic statistics. For
all these tasks some lower-level language with more efficient memory
handling will be much much better.


2014-03-08 8:13 GMT+09:00 Yoshiro Nagao <ng999 at yahoo.co.jp>:

> Hi Frank,
>
> Thank you very much for letting me know the important sites.
>
> I will see them and learn.
>
> Yoshiro
>
> --- On Fri, 2014/3/7, Frank Schwach <fs5 at sanger.ac.uk> wrote:
>
> > Hi Yoshiro,
> >
> > There is no such book (AFAIK) and it really boils down to what exactly
> it is you want to do.
> > One thing you will most likely be doing is working with BAM alignment
> files.
> > Check out BIo::SamTools
> > http://search.cpan.org/~lds/Bio-SamTools/lib/Bio/DB/Sam.pm
> > for that.
> > It's not part of BioPerl, so you need to install it separately.
> > You should then also look up samtools: http://samtools.sourceforge.net/
> > which is a very useful toolkit for working with sam/bam files, which you
> will certainly encounter. Again, this toolkit is not BioPerl (it's not
> written in Perl) but highly relevant to working with next-gen data.
> >
> >
> > Frank
> >
> >
> >
> >
> > On 07/03/14 01:21, Yoshiro Nagao wrote:
> > > Dear all,
> > > Please recommend a book(s) which contains information and codes
> > > about applying BioPerl to the output from next generation sequencers
> (NGS)
> > > (especially 454 and Illumina).
> > >
> > > Yoshiro Nagao
> > >
> > >
> > > _______________________________________________
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> >
> >
> >
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-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.