fastq_to_fasta(1) [debian man page]

FASTQ_TO_FASTA(1)						   User Commands						 FASTQ_TO_FASTA(1)

NAME

       fastq_to_fasta - Convert FASTQ files to FASTA files

DESCRIPTION

       usage: fastq_to_fasta [-h] [-r] [-n] [-v] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.13.2 by A. Gordon (gordon@cshl.edu)

       [-h]   = This helpful help screen.

       [-r]   = Rename sequence identifiers to numbers.

       [-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.

       [-i INFILE]
	      = FASTA/Q input file. default is STDIN.

	      [-o OUTFILE] = FASTA 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.

fastq_to_fasta 0.0.13.2 					     May 2012							 FASTQ_TO_FASTA(1)

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)