[Bioperl-l] Mummer parser and data anlysis

[shalabh sharma]

Hey Chris,
             Thanks for the reply , it was really useful.
Actually you are right, it is metagenomics sample. The thing is i've never
worked with that huge amount of data, so i am trying to test some alignment
programs (i am just trying to see if i can avoid blastx) so i am trying all
the available programs.

Blasting 200 million reads doesn't seems a right option (may be i will go
with assembly then blasting it).

Thanks
Shalabh


On Wed, Oct 20, 2010 at 11:45 AM, Chris Fields <cjfields at illinois.edu>wrote:

> On Oct 20, 2010, at 10:00 AM, shalabh sharma wrote:
>
> > Hi All,
> >        Is there any module for mummer in Bioperl?
> >
> > Also i need some suggestions and ideas (i think this is the best place to
> > ask).
> > I am working with huge data (around 200 million illumina reads), earlier
> i
> > was using blastx and other similar approaches to annotate but now i think
> > thats not possible, i would be very grateful if anyone can give me some
> idea
> > regarding this.
> >
> > Thanks
> > Shalabh
>
> Hard to say unless we know a little more about what you are attempting to
> do.  Not sure why you are using mummer here, but...
>
> This is something fairly well-covered in the literature for most use cases,
> and on places like seqanswers.  If you are doing something like aligning
> reads to reference genome(s) or set of gene models, you should be using
> something like bowtie/tophat, bwa, etc., with the output in SAM (BioPerl has
> perl wrappers for most of these modules).
>
> You can also do the same for metagenome analyses, but you may need to run
> BLAST and convert to SAM (maybe that's what you are doing?).  The samtools
> package comes with perl scripts to do that and can be further used to sort
> the matches, convert/index a BAM file for fast accession, etc.  From there
> you can then use tools like Bio::DB::SAM, R/BioConductor/RSamtools, or
> similar to access the sequences, find coverage statistics, run SNP calls,
> etc.
>
> And, for the record, we do have an experimental mummer parser, but I
> believe it lies in a branch at the moment (don't think it has been merged
> yet):
>
> http://github.com/bioperl/bioperl-live/tree/topic/bug-2701
>
> chris