.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.
.TH FASTX_CLIPPER "1" "September 2018" "fastx_clipper 0.0.14" "User Commands"
.SH NAME
fastx_clipper \- FASTA/Q Clipper
.SH DESCRIPTION
usage: fastx_clipper [\-h] [\-a ADAPTER] [\-D] [\-l N] [\-n] [\-d N] [\-c] [\-C] [\-o] [\-v] [\-z] [\-i INFILE] [\-o OUTFILE]
Part of FASTX Toolkit 0.0.14 by A. Gordon (assafgordon@gmail.com)
.TP
[\-h]
= This helpful help screen.
.IP
[\-a ADAPTER] = ADAPTER string. default is CCTTAAGG (dummy adapter).
[\-l N]       = discard sequences shorter than N nucleotides. default is 5.
[\-d N]       = Keep the adapter and N bases after it.
.IP
(using '\-d 0' is the same as not using '\-d' at all. which is the default).
.TP
[\-c]
= Discard non\-clipped sequences (i.e. \- keep only sequences which contained the adapter).
.TP
[\-C]
= Discard clipped sequences (i.e. \- keep only sequences which did not contained the adapter).
.TP
[\-k]
= Report Adapter\-Only sequences.
.TP
[\-n]
= keep sequences with unknown (N) nucleotides. default is to discard such sequences.
.TP
[\-v]
= Verbose \- report number of sequences.
.TP
If [\-o] is specified,
report will be printed to STDOUT.
.IP
If [\-o] is not specified (and output goes to STDOUT),
report will be printed to STDERR.
.TP
[\-z]
= Compress output with GZIP.
.TP
[\-D]
= DEBUG output.
.TP
[\-M N]
= require minimum adapter alignment length of N.
.TP
If less than N nucleotides aligned with the adapter \- don't clip it.
[\-i INFILE]  = FASTA/Q input file. default is STDIN.
.IP
[\-o OUTFILE] = FASTA/Q output file. default is STDOUT.
.SH SEE ALSO
The quality of this automatically generated manpage might be
insufficient.  It is suggested to visit
.IP
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
.P
to get a better layout as well as an overview about connected
FASTX tools.