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)