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

FASTQ-CLIPPER(1) User Commands FASTQ-CLIPPER(1)

NAME

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

DESCRIPTION

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.

OPTIONS

-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)
July 2015 fastq-clipper 1.1.2