fastx_clipper - FASTA/Q Clipper
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
- = 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).
- = Discard non-clipped sequences (i.e. - keep only sequences
which contained the adapter).
- = Discard clipped sequences (i.e. - keep only sequences
which did not contained the adapter).
- = Report Adapter-Only sequences.
- = keep sequences with unknown (N) nucleotides. default is
to discard such sequences.
- = 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.
- = Compress output with GZIP.
- = DEBUG output.
- [-M N]
- = require minimum adapter alignment length of N.
- If less than N nucleotides aligned with the adapter - don't
- [-i INFILE] = FASTA/Q input file. default is STDIN.
- [-o OUTFILE] = FASTA/Q output file. default is STDOUT.
The quality of this automatically generated manpage might be insufficient. It is
suggested to visit
to get a better layout as well as an overview about connected FASTX tools.