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0.108.0

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@derijkp derijkp released this 22 Feb 00:32
· 310 commits to master since this release
0.108.0
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Major highlights of the update are:

  • Addition of scywalker code for the analysis of single-cell ONT data
  • added cg viz_transcripts for making a nice visualision of transcript usage
  • ONT remora methylation support
  • added phased output for clair3 (using longphase)
  • added -iso_joint option : generic joint analysis support for iso calling
  • added -preset option for easily setting multiple (default) options for specific analyses
  • databases: added alphamissense annotation

Version opdates

  • isoquant 3.3.0
  • clair 1.0.4
  • sniffles 2.2 (also added option -minsvlen defaulting to 35 (not 50) so as to be more like previous versions in this respect
  • flair 2.0
  • flye 2.9.2
  • lumpy 0.3.1
  • medaka 1.4.4
  • nextflow 23.04.4

Some other changes/upgrades

  • jobs report maxmem, pct_cpu, bytes_read, bytes_written
  • ubam support
  • added cg_10x2tsv and cg tsv210x
  • html overview report plotly graphs can export svg
  • cg multicount added options -limit_geneids, -clip_geneid_version, -empty
  • cg keyvalue: added options -keyname and -valuename
  • cg_select: added option -optim memory to run big output summaries using little memory (though much slower)
  • optimization: shadowdirs
  • cg checktsv -checksort option
  • dirR updates/new libraries
  • added loc_lt, loc_lte, loc_gt, loc_gte
  • hisat2 binary

Full Changelog: 0.107.0...0.108.0

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