Program: fqclean filtrate/trim pair-end reads with adapter or with too many low-quality-base Version: v2.0 Contact: yerui [email protected]
Usage: fqclean in1.fq[.gz] in2.fq[.gz] out1.fq.gz out2.fq.gz
-n [f] read in which rate of N > [f] will be discarded. [0.1]
-q [f] read in which rate of low-quality-base > [f] will be discarded. [0.5]
-c [c] phred quality < [c] is treated as low quality base. [ 'F' ]
-p [i] [i] reads as a part to output. [0]
-m [i] minimum length of reads after cleaning. [30]
-u [s] UID types. ( NNNNNACT means 5bp barcode + 3bp fix
ACGNNNNN meads 3bp fix + 5bp barcode
NNNNNNNN meads 8bp barcode. )
-t [i] trim first N bp of reads (if has UID, trim N bp after UID) [0]