[Bioperl-l] Bio::Index::Fastq support for gzipped files

Albert Vilella avilella at gmail.com
Tue Feb 23 11:51:21 EST 2010


Maybe already answered somewhere but, do we have support for gzipped
fasta/fastq files?

Google tells me biopython does, but I couldn't guess for bioperl...



On Mon, Jan 4, 2010 at 9:59 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Bio::Index::Fastq, maybe?  To tell the truth, I haven't tried it since we refactored FASTQ parsing, so let us know if it doesn't work.
> chris
> On Jan 4, 2010, at 2:00 PM, Albert Vilella wrote:
>> Hi all,
>> What is the best way to index fastq files, so that once clustered, I
>> can provide a list of seq_ids and get
>> them back in fastq format from the indexed db?
>> Cheers,
>> Albert.
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