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PPanGGOLiN 2.0.0
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@JeanMainguy JeanMainguy released this 15 Jan 15:51
· 574 commits to master since this release
2.0.0
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Learn about vigilant mode.

New commands

  • projection: to annotate external genomes using an existing pre-computed reference pangenome (#119, see doc).

  • rgp_cluster: to cluster RGP based on their gene family content (#117, see doc).

  • metadata: add metadata linked to various pangenome elements using simple TSV files (#111, see doc).

  • the write command is split in two commands (#140):

    • write_pangenome: write outputs at the pangenome level (see doc)
    • write_genomes: write genome outputs with pangenome annotation. Three formats are available for outputs: table, GFF and JSON Proksee (#139, see doc).

  • utils: a small side command to generate a default configuration file for any commands (#112, see doc).

New features

  • A new, improved documentation hosted by readthedoc replacing the github wiki.
  • GFF export of genomes with pangenome annotation (#139, see doc).
  • JSON Map for Proksee to visualize interactively each genome and their pangenome annotation (#139, see doc).
  • Configuration file can now be used to set all or some parameters of PPanGGOLiN commands (#112, see doc).

Major change

BREAKING: New structure of the pangenome file to make it much lighter and faster to read (#110). ⚠️ Break the compatibility with PPanGGOLiN v1 pangenome HDF-5 files.

Minor change

  • Replacing Prodigal by pyrodigal for the annotation command (#138).
  • The context command has a window parameter to define the number of neighboring genes that are considered on each side of a gene of interest when searching for contexts (#137, see doc).
  • Replace all option keyword by synteny option keyword for draw –spots to draw spots with different RGP syntenies. Now all will draw all pangenome spots (#129)

Bug Fixes

  • Writing out only the RGP and spot of the gene with --projection (#130). Please note that, in version 2, the --projection parameter in the write command has been renamed to --table and now belongs to the write_genomes command (check the documentation of the write_genomes command for more details).
  • Make deterministic clustering (#116)
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