PombertLab/SYNY: SYNY-v1.2b

Changes

• run_syny.pl: Added the --min_asizecommand line option to filter out alignments/clusters smaller than integer value (e.g. --min_asize 5000)
• run_syny.pl: get_paf.pl, paf_metrics.py: Added the --no_sec command line option to filter out secondary alignments from minimap2 alignments.
• gff3_to_gbff.pl:
  • Annotations in the GFF3 files are now sorted by start positions in the GBFF files produced => annots in GFF3 files can be out-of-order
  • Fixed a bug that crashed the script when dealing with contigs without annotations.
  • Added preliminary support for AGAT-converted files (tested on a few user-provided files).
  • Added the --id command line option to label products by ID tags. Can be useful with GFF3 files that do not contain product descriptions.
• jgi_to_ncbi_gff.pl: New script that converts JGI GFF files to a NCBI-like GFF3 format compatible with gff3_to_gbff.pl.
• list_maker.pl: If /locus_tag and /db_xref="GeneID tags are missing from GBFF files, now checks for /gene tags and assign automatic locus_tags (format = $contig."_".$gene_counter).
• get_synteny.pl: Fixed a bug with median calculations if # of values < 2.