tgap/gap5

2008-11-12
2013-04-18
  • Sven Klages
    Sven Klages
    2008-11-12

    Hi,

    I still love gap4 for some  purposes, but it gets pretty slow when
    dealing with >500,000 454FLX-Reads ...

    Is there some kind of roadmap for the development of "gap5"?
    When will there be a "release candidate"?

    cheers,
    Sven

     
    • A good question!

      Progress has been very stop and start depending on the multitude of other interruptions, but I plan on getting a limited test release by the end of the year.

      Right now it works OK as a viewer of sequence. A more zoomed out graphical view of templates exists, but needs more work (it's a bit slow but I know ways of speeding it up considerably). Editing is coming along. Some things can be edited (basecalls obviously), but I haven't yet written the full gamut needed such as moving traces, inserting/deleting to consensus, etc.

      Then there are MANY missing features from Gap4. The most important are contig joining, contig breaking, tags/annotations and searching. That's quite fundamental though. I'm not sure how much will be done by the end of the year, but I plan on releasing whatever it's up to at that point as an alpha test at least for people to give feedback on.

      James

      PS. As for Gap4, I just fixed another issue with large databases where it couldn't cope with the .aux file over 2Gb. We successfully now have a Gap4 database with about 8 million FLX reads, but it's SLOW and memory hungry (about 7Gb).

       
    • Sven Klages
      Sven Klages
      2008-11-17

      huuh, .. 8 mio FLX reads? I don't want to "finish" such kind of
      project ;-)

      So I'll keep patiently waiting ..

      Thanks for the info,
      Sven