gap5 and caf files

  • cat17

    cat17 - 2010-06-10


    Have just read the recent paper on gap5 in bioinformatics. There you say it’s possible to save/export the assembly in caf format. We have the latest standalone package of gap5 but here it is not possible to this. Are there a newer version of gap5 folded into Staden source tree which can do this ? and if so, are the information on the quality of the reads also exported to the caf file ?


  • James Bonfield

    James Bonfield - 2010-06-10

    So the latest staden packages (eg staden-2.0.0b6) include gap5. This is the version you should use as it's had numerous improvements.

    Regarding caf though, it's indirectly supported. We provide a caf2baf perl script to convert to a simpler format which gap5 (strictly "tg_index") can then import. I've been using this strategy as a way of testing old school capillary assembly projects in gap5 as well as short-read data.

    You'll still need caftools though to go from gap4 to caf, which can be downloaded from the Sanger web site:


  • cat17

    cat17 - 2010-06-10

    Thanks for getting back to me so quickly.
    Forgive my confusion but your answer stroke me because in your bioinformatic manuscript you mention that "Gap5 may be used to output all or a portion of an assembly in ACE, SAM, BAM, BAF, CAF, fasta or fastq format." Does this still hold or is only though gap4 where I could get the CAF format?


  • James Bonfield

    James Bonfield - 2010-06-11

    Ah yes sorry I misread your comment and was thinking about import, not export.

    Gap5 recently gained the ability to save in CAF format, but I believe it did make it into the 2.0.0b6 release (rather than just the svn tree - revision 2060). I would state thought hat CAF really is not an ideal format to use as i's woefully inefficient for short read data.



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