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  • bowtie2 fun

    OK, folks

    Who here has used bowtie2-build on a database >4GB in size?

    When I try it with the latest Beta3 release with the 64Bit binary (which is supposed to allow databases > 4GB, it spits and dies during bowtie2-build with:

    Error: Reference sequence has more than 2^32-1 characters! Please divide the
    reference into batches or chunks of about 3.6 billion characters or less each
    and index each independently.

    Just wondering if anyone has successfully build an index using any releases of bowtie2 on large dbs.

  • #2
    For mappers that index the genomes, RTGinvestigator/bwa-0.6 are known to work with >4GB genomes. Agile is likely to support long genomes, too. Mappers that index the reads (e.g. maq) may work large genomes if one chromosome is no longer than 2GB.

    Supporting >4GB genomes is non-trivial and usually comes at a cost.
    Last edited by lh3; 11-18-2011, 04:27 PM.

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    • #3
      ok, this might be a dumb question but where did you get the bowtie2 src file? The manual say to look for "the filename that ends in "-src.zip". There is no bowtie....-src.zip file on the bowtie sourceforge site that I can find. Only the one for 0.12.7.

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      • #4
        nevermind. I found it. It just didn't have the "-src" in the name. Grrr.

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