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Improved re-squiggle and added 6mA model
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@marcus1487 marcus1487 released this 13 Feb 00:40
· 65 commits to master since this release
1.2
1afadeb

Major Tombo update includes:

  • Added N6-methyladenosine alternative model (in all sequence contexts)
  • Vastly improved re-squiggle results
    • Event segmentation and event-to-signal assignment parameter tuning
    • Specific parameters for DNA and RNA
  • Per-read statistics output
    • Including access via Tombo python API and random access to reads from genomic locations
  • Cleaner user experience
    • Converted to using mappy (minimap2 python API) in place of command line executable options
    • python 3 compatibility (addresses rpy2 conda install issues, numpy/cython memory leak and python2's slow painful death)
    • Simplified command line options (including some hidden advanced options for user generated models)
    • Unified plotting options
    • Better error and warning messages
  • General computational optimization
  • Added dampened fraction wiggle output (for variable coverage regions)
  • ROC plot command for testing results at a known motif
  • pyfaidx indexed genome FASTA access (for processing large genomes on limited resources)
  • Several important and minor bug fixes
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