fastq_quality_trimmer(1) [debian man page]

FASTQ_QUALITY_TRIMMER(1)					   User Commands					  FASTQ_QUALITY_TRIMMER(1)

NAME

       fastq_quality_trimmer - Filters sequences based on quality

DESCRIPTION

       usage:  fastq_quality_trimmer  [-h]  [-v]  [-t  N]  [-l	N] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.13.1 by A. Gordon (gor-
       don@cshl.edu)

       [-h]   = This helpful help screen.

       [-t N] = Quality threshold - nucleotides with lower

	      quality will be trimmed (from the end of the sequence).

       [-l N] = Minimum length - sequences shorter than this (after trimming)

	      will be discarded. Default = 0 = no minimum length.

       [-z]   = Compress output with GZIP.

       [-i INFILE]
	      = FASTQ input file. default is STDIN.

	      [-o OUTFILE] = FASTQ output file. default is STDOUT.  [-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.

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.

fastq_quality_trimmer 0.0.13.1					    April 2012						  FASTQ_QUALITY_TRIMMER(1)

KSSHELL(1)						      General Commands Manual							KSSHELL(1)

NAME

       ksshell -- an interactive kickstart shell

SYNOPSIS

       ksflatten [-i | --input INFILE]	[-o | --output OUTFILE]  [-v | --version VERSION]

DESCRIPTION

       ksshell is an interactive kickstart shell.  It optionally takes an input kickstart file as the basis, allows the user to specify additional
       kickstart commands, and then writes out the finished kickstart file to stdout or the given file name.  This program supports all the  usual
       readline niceties including tab completion of kickstart commands and their options, though not the values those options can take.

       In  addition to understanding all the kickstart commands, ksshell has some builtin commands of its own to make working with kickstart files
       in the context of a shell easier:

       .clear Clear the existing kickstart data, including any from INFILE.  This essentially starts you over from a blank state.

       .quit  Quit the interactive shell, either saving to the file given by OUTFILE or printing to stdout if none was given.

       .show  Print the current kickstart file state.

EXIT STATUS

       ksflatten returns 0 on success, and 1 if VERSION is incorrect.  If INFILE does not exist, a warning will be printed but the user will still
       be dumped to the interactive shell.

OPTIONS

       -i, --input INFILE
		 The name of the input kickstart file.

       -o, --output OUTFILE
		 Write the flattened kickstart file to OUTFILE, or stdout if no filename is given.

       -v, --version VERSION
		 Use this version of kickstart syntax when processing the file, or the latest if no version is given.

SEE ALSO

       ksvalidator (1), ksverdiff (1)

																	KSSHELL(1)