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.