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  1. Apr 01, 2020
  2. Mar 31, 2020
  3. Feb 23, 2020
  4. Dec 11, 2019
  5. Dec 09, 2019
  6. Dec 01, 2019
  7. Nov 07, 2019
    • Ian Fiddes's avatar
      Removing blat. · 2d04cd69
      Ian Fiddes authored
      Re-write the pairwise alignment step to use the parasail alignment library instead of BLAT.
      2d04cd69
  8. Nov 04, 2019
  9. Jan 09, 2019
  10. Nov 01, 2018
  11. Oct 23, 2018
    • Alana Alexander's avatar
      Update README.md · 1fbb4ee7
      Alana Alexander authored
      Removed "bedtools" from the necessary kent utilities list (because it is installed as a standalone)
      1fbb4ee7
  12. Sep 05, 2018
  13. Aug 24, 2018
  14. Aug 20, 2018
  15. Aug 01, 2018
  16. Jun 29, 2018
    • Joel Armstrong's avatar
      Add two dependencies · 3a53f0fc
      Joel Armstrong authored
      wigToBigWig is needed by part of the pipeline, and bd2k-python-lib
      seems to be needed. It was previously installed when installing toil,
      but later versions of toil don't need it anymore.
      3a53f0fc
  17. Mar 06, 2018
  18. Mar 05, 2018
  19. Dec 19, 2017
  20. Dec 04, 2017
    • Ian Fiddes's avatar
      More gene family collapse updates. · 666f9cc4
      Ian Fiddes authored
      1. Store metrics, added a plot.
      2. Perform a gene overlap analysis step at the end of consensus finding to ensure no novel predictions lead to problems.
      3. Fixed some bugs in the old implementation.
      4. Updated documentation to reflect these changes.
      666f9cc4
  21. Oct 05, 2017
  22. Oct 04, 2017
  23. Aug 25, 2017
  24. Aug 22, 2017
    • Ian Fiddes's avatar
      Turning UTRs off. · aa8c8ec7
      Ian Fiddes authored
      Not all augustus species have UTR models. In this case, the user needs to be able to turn this flag off.
      aa8c8ec7
  25. Aug 21, 2017
  26. Aug 16, 2017
    • Ian Fiddes's avatar
      Reworking GFF3 parsing. · 97acc471
      Ian Fiddes authored
      GFF3 parsing no longer relies on the slow GFF3 library, and instead relies on using the `-attrsOut` flag from `gff3ToGenePred` to construct features. A best attempt is made to parse GENCODE, Ensembl and NCBI format GFF3.
      
      Bring on the new edge cases!
      97acc471
  27. Jul 31, 2017
    • Ian Fiddes's avatar
      CAT now can handle protein FASTA! · a69c9593
      Ian Fiddes authored
      Protein FASTA files can now be introduced via the [PROTEIN_FASTA] section in the config file. Based on the genomes listed in the file, these will be aligned and used for AugustusTM(R) and AugustusCGP. This should greatly help with CGP predictions in more distantly related species.
      
      TODO:
      1. Talk to Mario and Stefanie about adjusting the CDS/CDSpart bonus/malus in the config files.
      2. Allow for arbitrary pre-generated hints files to also be included.
      a69c9593
  28. Jul 07, 2017
  29. May 31, 2017
  30. Mar 28, 2017
  31. Mar 21, 2017
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