Man page - fastq-clipper(1)

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Package: ea-utils
apt-get install ea-utils

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fastq-clipper - ea-utils: removes one or more adapter sequences from the fastq file

usage: fastq-clipper [options] <fastq-file> <adapters>

Removes one or more adapter sequences from the fastq file. Adapter sequences are colon-delimited. Stats go to stderr, unless -o is specified.

	-h		This help
	-o FIL		Output file (stats to stdout)
	-p N		Maximum difference percentage (10)
	-m N		Minimum clip length (1)
	-l N		Minimum remaining sequence length (15)
	-x [N]		Extra match length past adapter length,

N =-1 : search all N = 0 : search only up to adapter length

	-e		End-of-line (default)
	-b		Beginning-of-line (not supported yet)