[Bioperl-l] Bio::Index::Fastq - Interface for indexing (multiple) fastq files failure

KOVALIC, DAVID K [AG/1000] david.k.kovalic at monsanto.com
Tue Apr 6 15:38:11 EDT 2010


Thanks for information; it is good to know what the problem is.

I am afraid I am not much of a programmer so I am not liable to be much
help with any work switching out the back-end. I can however volunteer
for testing purposes if this helps at all.

I think this is just a case of NGS data volumes having overtaken a
previously adequate implementations.


-----Original Message-----
From: Chris Fields [mailto:cjfields at illinois.edu] 
Sent: Monday, April 05, 2010 6:57 PM
To: Peter
Cc: Jason Stajich; KOVALIC, DAVID K [AG/1000]; bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Bio::Index::Fastq - Interface for indexing
(multiple) fastq files failure

On Apr 5, 2010, at 6:15 PM, Peter wrote:

> On Mon, Apr 5, 2010 at 11:53 PM, Jason Stajich <jason at bioperl.org>
>> Hi David - I am not sure this is going to be the right tool for the
>> I'm concerned that none of the Bio::Index:: will really work for
>> Illumina/NGS size data because once you get beyond about 4M hash
>> keys things slow down quite dramatically and/or don't finish.
>> I think we have to consider SQLite implementations or some more
>> explicit way to handle larger keysize for hashes in the DB_File or
>> BerkeleyDB approach. A similar slow problem can be seen if you
>> just index a fastq converted fasta file from a single Illumina lane.
> Another example, and this was in Python rather than Perl, but
> SQLite got a thumbs up over an in house hash based approach:
> I think a new SQLite based Bio* OBF successor to the existing
> BDB based OBDA standard for indexing files could be very interesting.
> Peter

Would be nice to get some ideas performance-wise with some data sets.
SQLite is a very easy option (I'm using it routinely as well).


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