config.yaml

# ------ Samples ------
samples: ['M_P0','M_P1'] # specify a list samples to use or '*' to use all samples

# ------ Resources ------
threads : 20 # single task nb threads

# ------ Assembly parameters ------ 
data: /path/to/input_reads # path to data folder

# ----- Annotation database -----
cog_database: /path/to/rpsblast_cog_db/Cog  # COG database

# ----- Binner ------
binner: "concoct"

# ----- Binning parameters ------
concoct:
    contig_size: 1000

read_length: 150
assembly: 
    assembler: spades
    k: [77]
    mem: 2000
    threads: 24

# ----- BayesPaths parameters ------
bayespaths:
    nb_strains: 5
    nmf_runs: 1
    max_giter: 1
    min_orf_number_to_merge_bins: 18
    min_orf_number_to_run_a_bin: 10
    percent_unitigs_shared: 0.1

# ----- DESMAN parameters ------
desman:
    execution: 1
    nb_haplotypes: 10
    nb_repeat: 5
    min_cov: 1