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

[Frank Schwach]

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
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



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