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SYNY-v1.0
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@Pombert-JF Pombert-JF released this 29 Apr 19:31
· 153 commits to main since this release
1.0
e90b61b

Stable release

Changes:

Misc:

  • Fixed output directory bug in run_syny.pl when using a deep tree
  • Fixed abs_path() issue in setup_syny.pl that caused incomplete paths in the output configuration file
  • Created check_mp_colors.py to list/plot color palettes available on the system (Fedora 40/Ubuntu 22.04 matplotlib palettes are not the same - 170 vs. 166) + added color palette plot
    (Images/python_color_palettes.png)
  • Fixed out of bounds barplot legends
  • Added font size options --bfsize/--dfsize options for barplots/dotplots
Circos:
  • Contigs from the reference genome are now visually distinct and are labelled by roman numerals. Other contigs are labelled by arabic numerals.
  • Added --orientation option (possible values: normal, inverted, both) + removed the now obsoleted --no_invert/--no_normal options
  • Added --no_cticks option to disable ticks in Circos plots.
  • added --no_ntbiases option to disable nucleotide bias subplots.
  • Changed the default Circos plot mode to pairwise (--circos pair); concatenated plots can take a while to compute and are not always useful.
  • Circos figures are now plotted in --orientation normal by default instead of both normal/inverted => less wasteful.
  • Renamed the .genotype files generated by SYNY as .karyotype to match the nomenclature used by Circos
Assets 2
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