HEADER = 1
  SCAFFOLD = [ /(.+)/ /scaf_/scaffold/ ]
  CONTIG = [ /(.+)/ /ctg_/contig/ ]
  • To use a file as a source of scaffold name synonyms for import_sequence_synonyms.pl, [FILES] SCAFFOLD_NAMES must be set and the HEADER flag may be used to indicate that the file has a header row that should be skipped during import.
  • Alternatively Match and replace regular expressions may be defined for SCAFFOLD and/or CONTIG names to automatically generate a file of synonyms during sequence import.