ASSEMBLY_KMERS

ASSEMBLY_KMERS section in PARAMS can optionally be used to assembly significant kmers obtained by pcadapt or/and lfmm.

Contigs are assembled by iKISS using mergeTags from dekupl package https://github.com/Transipedia/dekupl-mergeTags.

Chose minimal overlap size “OVERLAP_SIZE” allowed to assembly kmers.

Feel free to filter contigs by size “FILTER_CONTIG_SIZE”.

Assembled contigs could be mapped activating MAPPING_CONTIGS. This mapping can be launch versus a REF reference file using bwa-mem2 by default. Reference file used in this step can be a different reference from MAPPING_KMERS options. Feel free of change parametters of mapping using MAPPING_OPTIONS

Assembled contigs could be used by blastn against a database, you can also try to annotate them!

PARAMS:
   ASSEMBLY:
      OVERLAP_SIZE : 15
      FILTER_CONTIG_SIZE : 100
      MAPPING_CONTIGS: True
      # if MAPPING_CONTIGS is activate, ikiss maps contigs vs REF using bwamem2
      REF: 'reference.fasta'
      MAPPING_OPTIONS : ""