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fastx_clipper - FASTA/Q Clipper

FASTX_CLIPPER(1) User Commands FASTX_CLIPPER(1)

NAME

fastx_clipper - FASTA/Q Clipper

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)
[-h]
= This helpful help screen.
[-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.
(using '-d 0' is the same as not using '-d' at all. which is the default).
[-c]
= Discard non-clipped sequences (i.e. - keep only sequences which contained the adapter).
[-C]
= Discard clipped sequences (i.e. - keep only sequences which did not contained the adapter).
[-k]
= Report Adapter-Only sequences.
[-n]
= keep sequences with unknown (N) nucleotides. default is to discard such sequences.
[-v]
= Verbose - report number of sequences.
If [-o] is specified,
report will be printed to STDOUT.
If [-o] is not specified (and output goes to STDOUT), report will be printed to STDERR.
[-z]
= Compress output with GZIP.
[-D]
= DEBUG output.
[-M N]
= require minimum adapter alignment length of N.
If less than N nucleotides aligned with the adapter - don't clip it.
[-i INFILE] = FASTA/Q input file. default is STDIN.
[-o OUTFILE] = FASTA/Q output file. default is STDOUT.

SEE ALSO

The quality of this automatically generated manpage might be insufficient. It is suggested to visit
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
to get a better layout as well as an overview about connected FASTX tools.
August 2017 fastx_clipper 0.0.14