fastx_clipper(1) 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 ([email protected])
= 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 clip it.
[-i INFILE] = FASTA/Q input file. default is STDIN.
[-o OUTFILE] = FASTA/Q output file. default is STDOUT.