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SYNY-v1.1
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@Pombert-JF Pombert-JF released this 16 May 11:43
· 105 commits to main since this release
1.1
845ecc4

Changes:

Additions:
  • SYNY now generates linear maps (aka linemaps) from PAF files with linear_maps.py.
  • Added support for MashMap3 genome alignments. Mashmap can be selected instead of minimap with --aligner mashmap. It runs in a smaller memory footprint than minimap (if using its default percentage identity of 85%). It does not product exact alignments however.
  • Added the option to exclude contigs by name matching regular expression(s): e.g. --exclude '^AUX' '^CPGT'.
  • Added an alternate SYNY installation method that does not require sudo privileges by leveraging conda packages.
Fixes:
  • Fixed the The number of annotation files (2) does not equal the number of protein files (1) error => rewrote the corresponding segment and removed the obsoleted subroutine.
  • Fixed the unreliable $diamond_check in get_homology.pl (i.e. replaced which by command -v).
  • Changed Perl dependency Roman => Text::Roman in nucleotide_biases.pl.
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