[Bioperl-l] Bio::Assembly::IO

Fungazid fungazid at yahoo.com
Fri Jun 26 07:59:06 EDT 2009


I received an ACE file containing newbler assembly of 454 cDNA reads, and a corresponding phd.ball file. I was able to view and manipulate the contigs in this assembly using Consed on linux. Consed required ~1.5GB RAM, and the assembly was loaded within ~2 min. 
I would like to parse the assembly within my code (preferentially in Perl, but not necessarily), to fetch all read sequences for each contig, nucleotide quality, alignment to consensus, etc. 
I am trying to use Bio::Assembly::IO , but it eats more than my entire RAM (3GB), and is extremely slow (~1 hour before it crashes).
Maybe you have an idea ?
In addition, do you maybe aware of other non-visual parsers of ACE assembly format for Perl or other languages

Many thanks,



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