config.yaml

---
# path to conda on my own machine (adapt for yours)
condapath: "/opt/miniconda3/condabin"
condaenv: "InSilico_PCR"

# threads for parallel tasks
thr: 80

# threads for compression
pigt: 8

# max mem for BBMap tasks
mem: "8g"

# split data in 500k read bins (500000x4=2000000)
lines: 2000000

# Mock Community url for raw data
host: "https://nanopore.s3.climb.ac.uk/"
infile: "Zymo-PromethION-EVEN-BB-SN.fq.gz"

# primer pairs to extract reads corresponding to 16S amplicon(s)

forwardp: "AGAGTTTGATCMTGGCTCAG"
forwardl: "27F"
reversep: "CGGTWACCTTGTTACGACTT"
reversel: "1492Rw"

#forwardp: "GACTCCTACGGGAGGCWGCAG"
#forwardl: "337F"
#reversep: "GACTACHVGGGTATCTAATCC"
#reversel: "805R"

#forwardp: "GTGYCAGCMGCCGCGGTAA"
#forwardl: "515FB"
#reversep: "CGGTWACCTTGTTACGACTT"
#reversel: "1492Rw"

# stringent primer finding to avoid noisy reads
cut: 0.8

# exclude the 1% shortest reads, change to 0 to disable filtering
filterperc: 0.01