# version: 6a90598-dirty
#/Users/mario/assembly-tools/bin/layout --overlaps_format=mhap -r /Users/mario/assembly-tools/npore_ecolli_reads/reads-nmeth-all_2d.fasta -x overlaps.mhap -v 1
# filter reads parameters
READS_MIN_LEN: 3000

# trimming parameters
READ_LEN_THRESHOLD: 100000
MAX_READS_IN_TIP: 2
MAX_DEPTH_WITHOUT_EXTRA_FORK: 5

# bubble popping parameters
MAX_NODES: 750
MAX_DISTANCE: 7500000
MAX_DIFFERENCE: 0.250000

# contig extraction parameters
MAX_BRANCHES: 18
MAX_START_NODES: 100
LENGTH_THRESHOLD: 0.200000
QUALITY_THRESHOLD: 0.200000