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ssake(1) [debian man page]

SSAKE(1)						      General Commands Manual							  SSAKE(1)

NAME

       ssake - assembling millions of very short DNA sequences

SYNOPSIS

       Progressive assembly of millions of short DNA sequences by k-mer search through a prefix tree and 3' extension.

OPTIONS

       -f     Fasta file containing all the [paired (-p 1) / unpaired (-p 0)] reads (required) paired reads must now be separated by ":"

       -s     Fasta file containing sequences to use as seeds exclusively (specify only if different from read set, optional)

       -m     Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default -m 16)

       -o     Minimum number of reads needed to call a base during an extension (default -o 3)

       -r     Minimum base ratio used to accept a overhang consensus base (default -r 0.7)

       -t     Trim up to -t base(s) on the contig end when all possibilities have been exhausted for an extension (default -t 0)>

       -p     Paired-end reads used? (-p 1=yes, -p 0=no, default -p 0)

       -v     Runs in verbose mode (-v 1=yes, -v 0=no, default -v 0, optional)

       -b     Base name for your output files (optional)

       ============ Options below only considered with -p 1 ============

       -d     Mean distance expected/observed between paired-end reads (default -d 200, optional)

       -e     Error (%) allowed on mean distance   e.g. -e 0.75  == distance +/- 75% (default -e 0.75, optional)

       -k     Minimum number of links (read pairs) to compute scaffold (default -k 2, optional)

       -a     Maximum link ratio between two best contig pairs *higher values lead to least accurate scaffolding* (default -a 0.70, optional)

       -z     Minimum contig size to track paired-end reads (default -z 50, optional)

       -g     Fasta file containing unpaired sequence reads (optional)

SEE ALSO

       /usr/share/doc/ssake/SSAKE.readme between

AUTHORS

       This  manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others).  Permission is granted
       to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
       the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

								   January 2008 							  SSAKE(1)

Check Out this Related Man Page

OPTIMIZE2BW(1)							 ExactImage Manual						    OPTIMIZE2BW(1)

NAME

       optimize2bw - automatic thresholder of the ExactImage toolkit

SYNOPSIS

       optimize2bw [option...] {-i | --input} input-file  {-o | --output} output-file

       optimize2bw --help

DESCRIPTION

       ExactImage is a fast C++ image processing library. Unlike many other library frameworks it allows operation in several color spaces and bit
       depths natively, resulting in low memory and computational requirements.

       optimize2bw reads image files and performs automatic thresholding and optional scaling on the data. It is useful for long term archiving of
       documents that have to be stored in sub-byte black and white data to reduce storage requirements.

OPTIONS

       -i file, --input file
	   Read image from the specified file.

       -o file, --output file
	   Save output image to the specified file.

       -n, --denoise
	   Remove ("denoise") single bit pixel noise.

       -d n, --dpi n
	   Scale the image to the specified resolution.

       -h n, --high n
	   Set high normalization value.

       -l n, --low n
	   Set low normalization value.

       -r n, --radius n
	   Set "unsharp mask" radius. The default is 0.

       -s n, --scale n
	   Set output scale factor. The default is 1.0.

       -sd x, --standard-deviation x
	   Set standard deviation for Gaussian distribution. The default is 0.0.

       -t n, --threshold n
	   Set threshold value. The default is 0.

       --help
	   Display help text and exit.

EXAMPLES

	   $ optimize2bw -i logo.jpg -o logo.tif
	   Scale: 0

SEE ALSO

       exactimage(7)

AUTHORS

       Jakub Wilk <jwilk@debian.org>
	   Wrote this manual page for the Debian system.

       http://www.exactcode.de/site/open_source/exactimage/
	   This manual page incorporates texts found on the ExactImage homepage.

COPYRIGHT

       This manual page was written for the Debian system (and may be used by others).

       Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 or (at
       your option) any later version published by the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL-2.

optimize2bw							    09/09/2013							    OPTIMIZE2BW(1)
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