C++ libraries for NGS data and such

[pasta]

Hi there,

I am a Delphi/php guy and I am new using C++ in bioinformatics.
I am looking for the most mature c++ library than can deal with Next Generation Sequecing data and common file formats used in biology(gbk, ptt, fasta, sam, etc...).

Do you have any idea ?

Thank you for your help,

cheers,

toni

[pasta]

Partially solved for SAM format: A C library is available on SAMtools website (http://samtools.sourceforge.net/samtools-c.shtml), dumb me !!
Any other good library for Gbk, fasta and ptt ?

[kmcarr]

The NCBI Toolbox? Not a C++ programmer myself so I can't say much more about them.

http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi

[colindaven]

Try http://www.seqan.de/

[pasta]

Thank you guys for your answers
The NCBI toolbox is maybe a bit limited but Seqan looks pretty cool.

Thanks++

toni

[n00c]

SeqAn is a well-rounded and a well-designed library (there's even a book about it: http://www.amazon.com/Biological-Seq.../dp/142007623X, which I found to be a useful reference), but if you want to work with SAM/BAM format specifically, I would seriously recommend studying the C functions in Samtools for manipulating SAM-/BAM-formatted data. Looking at Samtools code is useful because (a) it was written by the author of SAM format, and (b) in Samtools code, you can find many examples on how to manipulate the exposed data structures.

There is also a C++ library called Bamtools (http://sourceforge.net/projects/bamtools/), but so far my preferred way has been to use a custom-written lightweight C++ wrapper for the C interface exposed by "bam.h" from Samtools.

License-wise, Samtools and Bamtools are under MIT licenses, and SeqAn is under BSD.

[pasta]

Thank you guys and n00c for your answer .

Cheers,

Toni

[schmima]

Partially solved for SAM format: A C library is available on SAMtools website (http://samtools.sourceforge.net/samtools-c.shtml), dumb me !!

in case you get angry while trying to read the "documentation" of the C-API, have a look at bamtools instead (on samtools.com on the right there's a section "other language bindings" - bamtools is the one in c++). Found it way easier to understand and use


[EDIT - uups - sorry for the double post...]

[Simon Anders]

Any specific reason you want to use C++? If you want to develop general-use high-performance bioinformatics tools, it is the way to go, of course -- but in most cases, a scripting language might be the better choice as it allows more rapid development and gives a performance sufficient for most use cases.

Hence, maybe have a look at our Python framework, HTSeq: http://www-huber.embl.de/users/anders/HTSeq/

[schmima]

I would agree with Simon - used/using python quite a lot (there's also a SAM/BAM interface). However - personally I like to write certain things in c++ instead of python - my code is better organised and I normally think more before writing it and regarding memory efficiency and speed, c++ is way better than python (at least in my programs and scripts).

[pasta]

in case you get angry while trying to read the "documentation" of the C-API, have a look at bamtools instead (on samtools.com on the right there's a section "other language bindings" - bamtools is the one in c++). Found it way easier to understand and use


[EDIT - uups - sorry for the double post...]

You read my mind - thanks for your tip !


@Simon: Thanks but I am working on large files and I want to make it very memory efficient.

[pasta]

*Just for the community*
I also found TIGR++ :http://www.cbcb.umd.edu/software/pirate/tigr++.shtml

C++ class library used by several TIGR genefinders and other packages. Covers string & sequence processing, math/statistics, many efficient data structures, GFF parsing, sorting, and I/O.

Cheers

toni