cleanhp - Remove hairpin reads

Synopsis

$ dnmtools cleanhp [OPTIONS] <read-1.fastq> <read-2.fastq>

 -o, -output

output filename prefix [required]

 -s, -stat

stats output filename [required]

 -h, -hairpin

maximum hairpin rate

 -check

check for hairpin contamination

 -n, -nreads

number of reads in initial check

 -c, -cutoff

cutoff for calling an inverse duplication(default: 0.95)

 -i, -ignore

length of read name suffix to ignore when matching

 -v, -verbose

print more run info to the terminal while the program is running

 -h, -hist

write a histogram of hairpin matches to this file