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"?
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.
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).
huuh, .. 8 mio FLX reads? I don't want to "finish" such kind of
So I'll keep patiently waiting ..
Thanks for the info,