config.yaml

# Modify The following paths based on your input/output
# 'barcode_files' is only required if you have set 'basecall:perform_basecall' to false
results: "results/"
basecall_files: "data/fast5/"
barcode_files: "data/fastq"
reference_database: "/project/brookings_minion/reference_databases/zymogen_reference.fasta"


# -------- DEFAULT VALES --------
# 'guppy_container:' not be changed, unless you know of another instance of guppy_container
guppy_container: "/project/brookings_minion/guppy_container.sif"

basecall:
    # should basecalling be done?
    perform_basecall: True
    # set this variable to the configuration name you would like to use with basecalling
    # Fast basecalling is dna_r9.4.1_450bps_fast.cfg
    configuration: "dna_r9.4.1_450bps_hac.cfg"

barcode:
    # set the barcode_kit variable to the name of the barcoding kit you will be using
    kit: "EXP-PBC096"

# Rule move_low_reads
cluster:
    # clusters with 3 or fewer reads will be excluded from spoa
    min_reads_per_cluster: 3
    # The default value for divergence threshold under rule filter_id_reads_mapped_sequence
    divergence_threshold: 0.05

cutadapt:
    # set the error rate, 3' adapter, and 5' adapter to use with cutadapt (trimming reads)
    error_rate: 0.15
    three_prime_adapter: "ACTTGCCTGTCGCTCTATCTTCTACCTTGTTACGACTT"
    five_prime_adapter: "TTTCTGTTGGTGCTGATATTGCAGRGTTYGATYMTGGCTCAG"

isONclust:
    aligned_threshold:  0.85
    min_fraction:  0.95
    mapped_threshold:  0.70
    min_shared: 55

nanofilt:
    # Minimum and maximum filtering length to be used
    max_filter: 1700
    min_filter: 1200
    min_quality: 7