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2.0.0
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@macmanes macmanes released this 26 Jul 12:23
· 347 commits to master since this release
2.0.0
c069d2d

This is a major new release and everybody is encouraged to update. Because this release contains tons of new functionality, it's entirely possible that a simple git pull from your existing repo will fail (sorry about that). Better to install in a new location, and potentially delete the old. The install from fresh, see http://oyster-river-protocol.readthedocs.io/en/latest/aws_setup.html

Change log

  • The use of LinuxBrew has been removed, in favor of conda. Dependencies are now managed by conda. You will need to launch the orp_v2 conda environment, which is created by make, before assembling.
  • The final assembly is now called $RUNOUT.ORP.fasta.
  • Shannon has been removed, and TransABySS has been added in it's place. MANY users (and myself) have struggled with the RAM use and runtime of Shannon. TransABySS is much faster, and uses much less RAM.
  • Diamond is leveraged for transcript recovery. It had been noted by some users that a few "real" transcripts were getting lost during the OrthoFuser steps.. Diamond, which is run after, recovers those.
  • cd-hit-est is now run at the end of the assembly process, using a 98% threshold. This removes many identical (or nearly so) transcripts from the assembly.
  • The report that is printed at the end of the assembly has been enhanced.
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