[Bioperl-l] Limitations for Bio::DB::Fasta

Ki Baik hkbaik at gmail.com
Mon Jul 7 18:12:12 UTC 2014

I'm trying to index a large fasta file that I downloaded from NCBI's ftp
site. The size of the fasta file is 700GB. I'm trying to use Bio::DB::Fasta
to index this file. When the index file hits around 10GB, it seems to hang.
I'm wondering if there is a limit on the fasta file size it can index.

Also, how does Bio::DB::Fasta compare to Bio::Index::Fasta? Is one better
for large fasta files? Are there any other indexing schemes I can use
instead of these modules? Any information would be appreciated.


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