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

[Fields, Christopher J]

Yoshiro,

I just want to point out, I have seen use of perl, python, etc with NGS analysis.  The majority of their use is in parsing through large data sets.  However, in many cases (e.g. Bio-Samtools) there are lower-level bindings to the same C code that is used with the command-line tools (e.g. samtools).  Other tools have the same capability (e.g. tabix, VCFtools, etc).  Pure perl and python cod have both been used to munge through FASTQ, FASTA, SAM, and VCF output as well (with built-in regex support they are both great at text parsing, much more so than C).

So, I don’t completely agree with Alexey, in that you definitely can work with NGS data using perl.  BioPerl is an unfortunate exception, in that the current OO nature of the code is a problem (terribly inefficient).  We welcome any input into this area, but it essentially needs a bottom-up redesign in this area.

chris

On Mar 11, 2014, at 12:41 AM, Yoshiro Nagao <ng999 at yahoo.co.jp> wrote:

> Hi Alexey,
> 
> Thank you very much for your comment.
> It seems to me, from what Frank wrote, that Bioperl just provides wrappers from which assembled modules are called...
> 
> Anyway, I will consider whether to use lower level language (such as C) or compile Perl codes by using a commertial compiler.
> 
> Thanks again,
> 
> Yoshiro
> 
> --- On Tue, 2014/3/11, Alexey Morozov <alexeymorozov1991 at gmail.com> wrote:
> 
>> 
>> 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
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> 
>>> -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
>> 
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>> 
>> 
>> -- 
>> Alexey Morozov,
>> LIN SB RAS, bioinformatics group.
>> Irkutsk, Russia.
>> 
> 
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