config.yaml

prefix: "default"
threads: 48
tmp: "./tmp"

# int cutoff of freq number for select beads; 0 means output all beads
beadSelect: 10
distCutoff: 0.04
divideSH: 10

BB_LIST: "REF/barcode.list"
REF_GEN: "REF/ncbi.5Ref.fasta"

REF_FA: "REF/ncbi.5Ref.fasta"
REF_ID: "REF/ncbi.5Ref.faID"

REF_nt: "/REF/blast_nt/nt"
REF_silva: "REF/silva132/combine/SILVA_132_SSU_LSU_tax_DNA.blast"

sampleType: "F" # F(ungi) or B(acteria)

### adapters
AdRCA: AAGTCGGACGCTGATAAGGTCGCCATGCCTCTCAGTACTCCGACTT
AdFw:
AdRv:
A_primer_list_to_remove:
A_primer_fa_to_find: "REF/primers.fa"
### Primers
pmrFwd:
pmrRev:
### method selection
method:
  cluster:
    mash: False
    dups: False
    bb1m: True
    test: True
    circos: True
  assemble:
    mode: "megahit"

### params

#### mash dist params
p_dist_k: 31
p_dist_s: 1000

p_dist_min: 0.02
p_dist_max: 0.04

#### cluster cutoff
p_cluster_minR: 5
p_cluster_maxR: 1000
p_cluster_topB: 0
p_cluster_ranP: 0

#### community level
p_dist_lv: 1

#reads per bead threashold
p_rpb_min: 100
#reads/beads per cluster threashold
p_rpc_min: 100
p_bpc_min: 0

#Assembly
p_asm_min: 500
p_asm_mem: 10000000000
p_asm_cpu: 4

#VSEARCH
p_VS_preClust: 99.9
p_VS_postClust: 99

#Circos
p_cc_zoom: 1
p_cc_cut:  97

######################

### Thread control
thread:
  manualDivide: 2
  pigz: 4
  fastp: 4
  spades: 4
  megahit: 1
  vsearch: 16
  blastn: 16
  athena: 24