Provided by: fastx-toolkit_0.0.14-6_amd64
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 (firstname.lastname@example.org) [-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.
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.