dentist.greedy.yml

# WARNING: Use with care!
#          Always validate the closed gaps (e.g. manual inspection).

# NOTE: The workflow creates an intermediate assembly
#   `workdir/{output_assembly}-preliminary.fasta` that contains all closed
#   gaps, i.e. before validation. It is accompanied by an AGP and BED file.
#   You may inspect these files for manual selection of the closed gaps to
#   get maximum sensitivity. After selecting viable closed gaps, you have
#   to adjust the file `workdir/skip-gaps.txt` to reflect your wishes.

__default__:
    verbose: 2
    allow-single-reads: true
    best-pile-up-margin: 1.5
    existing-gap-bonus: 3.0
    join-policy: contigs
    min-reads-per-pile-up: 1
    min-spanning-reads: 1
    proper-alignment-allowance: 500