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Version v1.5.0. Fixes #290. Fixes #293 #294

Merged
merged 64 commits into from
Sep 21, 2023
Merged

Version v1.5.0. Fixes #290. Fixes #293 #294

merged 64 commits into from
Sep 21, 2023

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gbouras13
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@gbouras13 gbouras13 commented Sep 21, 2023

  • Adds support for pyrodigal-gv implementing prodigal-gv as a gene predictor (pyrodigal-gv and prodigal-gv). This can be specified with -g prodigal-gv.
  • Thanks to @althonos and @apcamargo for making this possible, and to @asierFernandezP for raising this as an issue in the first place here in Error calling tRNAscan-SE #290.
  • Adds checks to determine if your input FASTA has duplicated contig headers from Expanding initial checks for user friendliness #293 here. Thanks @thauptfeld for raising this.
  • -g prodigal and -g prodigal-gv should be much faster thanks to multithread support added by the inimitable @althonos.
  • Genbank format output will be designated with PHG not VRL (following this issue FLiP phages are missing from the database RyanCook94/inphared#22).
  • The _length_gc_cds_density.tsv and _cds_final_merged_output.tsv files now contain the translation table/genetic code for each contig (usually 11 but now not always if you use pyrodigal-gv).
  • --skip_mash flag added to skip finding the closest match for each contig in INPHARED using mash.
  • --skip_extra_annotations flag added to skip running tRNA-scanSE, MinCED and Aragorn in case you only want CDS predictions and functional annotations.

@gbouras13 gbouras13 merged commit 22747b7 into master Sep 21, 2023
@gbouras13 gbouras13 deleted the dev branch September 21, 2023 06:10
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