config_shag.yaml

##### Run configuration #####

run_name: Shag1_10birds
output_path: '/Users/s1680070/VirusEvolution Dropbox/Aine OToole/aging-mice/shag_clock/Shag1_10Birds/analysis/'
input_path: '/Users/s1680070/VirusEvolution Dropbox/Aine OToole/aging-mice/shag_clock/Shag1_10Birds/fastq_pass/'

##### Read length filters #####

min_length: 140
max_length: 550

##### Genes amplified #####

genes:
  Locus2: Locus2
  Locus5: Locus5
  Locus7: Locus7

##### Reference files #####

references_file: references/carbo_loci_converted.fasta
substitution_matrix: references/substitution_matrix.txt
cpg_csv: references/shag_cpg_sites.csv


##### Porechop options #####

require_two_barcodes: "False"
discard_middle: "True"
split_reads: "False"
discard_unassigned: "False" #default keep unassigned, change to --discard_unassigned if you don't want to see unbarcoded reads
barcode_set: "pcr" # [native,rapid,all], defaults to `native`, `all` is much slower
limit_barcodes_to: #barcode csv string e.g. NB01,NB02,NB03,NB04,NB05,NB06
barcode_threshold: 70
barcode_diff: 3

##### Barcodes in run #####

barcodes:
  - BC01
  - BC02
  - BC06
  - BC07
  - BC09
  - BC11
  - BC12
  - BC30
  - BC35
  - BC52
  - BC59
  - BC62
  - BC81
  - BC83
  - BC85
  - BC90