Assets 2

Bugfix release. Avoid bailing if Refiner could not produce a consensus from the family sequence set.

@rmhubley rmhubley released this May 12, 2017 · 6 commits to master since this release

Assets 2
  • Bugfix release. Fixes a bug that will cause RepeatModeler to exit if no new repeats are detected after round-2. In typical runs repeats will continue to be discovered even up to the last round and this bug will not be exercised.

@rmhubley rmhubley released this Apr 6, 2017 · 9 commits to master since this release

Assets 2
  • RepeatModeler employs a genome sampling approach that is based
    on a random number generator. In this release of RepeatModeler
    we print out the random number generator seed at the start of
    a run. This number can be used with the "-srand ####" flag in future
    runs to exactly reproduce the samples taken from a given database.

  • The final output files are now placed in the same directory as
    the input database.

  • An additional output file is now generated containing the seed
    alignment for each discovered family. This alignment is the source
    of the final consnesus and is stored in a Dfam compatible Stockholm
    file. The new output files are named <database_name>-families.fa and
    <database_name>-families.stk.

  • Support for Dfam_consensus has been built into this release. Two
    utilities dfamConsensusTool.pl and renameIds.pl can be found in the
    RepeatModeler util/ directory. The dfamConsensusTool script enables
    one to upload curated seed alignments to the open Dfam_consensus
    database from the command line. The renameIds script simplifies
    the process of coming up with unique identifiers for a set of
    RepeatModeler generated families given a naming template.