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Interactive assembly and analysis of RAD-seq data sets
Sep 15 2016 22:56
has now been released:
big speed improvements to steps 3 and 6
threaded clustering/mapping within samples
better error reporting
better memory handling in step3
fixed problem with branching and changing mindepth_majrule
fix to final indel filter (it was over-counting/filtering indels)
fix to alignment splitting bug for pairgbs data where pairs were not being split and aligned separately for reverse complement matched pairs.
fix to progress bar counter sometimes not finishing in step 6.
I think the new version will fix your problem, and run much faster.