config.yml

ncbi_reference_accession: NC_008155.1
#sample:
my_email: aaron.phillips@adelaide.edu.au

fast_file: fastq # fastq/fasta/fastq.gz/fasta.gz

assembler:
  - flye
  - unicycler

rand_seed:
number_reads: 3000
read_min_length: 5000
                    
flye_parameter: --nano-raw 
    # --nano-raw    = ONT reads base-called prior to the release of Guppy5+
    # --nano-corr   = corrected ONT reads
    # --nano-hq     = high quality ONT reads that have been base-called with Guppy5+
    # --pacbio-raw  = PacBio CLR reads
    # --pacbio-corr = corrected CLR reads
    #--pacbio-hifi  = PacBio HiFi reads

minimap2_parameter: map-ont
    # map-pb   = PacBio CLR reads
    # map-ont  = ONT long reads 
    # map-hifi = PacBio HiFi reads

read_quality: 1
    # minimum PHRED-based quality score for read alignment

chloroplast_size: 135000  # estimate of chloroplast genome size; also used as the upper limit of read length

# Chlorplast QC check parameters
#chloroplastSizePC: 0.85     # If assembled genome <(chloroplastSize*chloroplastSizePC), will not pass.
#chloroplastIdentityPC: 0.85 # If the identity (measured by DNADiff) of assembled genome to reference genome <chloroplastIdentityPC, will not pass

cpus: 4 # Max CPUs to use in a job.