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FAHASH

FAHASH

Section: User Commands (1) Updated: April 2008
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NAME

fahash - sequence hash builder for reverse e-PCR

 

SYNOPSIS

fahash [-hV] -b hash-file [-w wdsize] [-f period] [-F fragment_min,fragment_max] [-k] [-c cachesize] [-v 1|2] famap-file ...

fahash [-hV] -T hash-file [-o outfile]

 

DESCRIPTION

The program fahash is part of the e-PCR suite and is used to build hash-files, and output word usage statistics for reverse e-PCR searches.

 

OPTIONS

-b hash-file
Build hash tables (hash-file) from sequence files,
-T hash-file
Print word usage statistics for hash-file
-o outfile
Write output to file `outfile'

 

build-options:

-w wordsize
Set word size when building hash tables
-f period
Set discontiguity when building hash tables
-k
Skip repeats when building hash-file
-F min,max
Set watermarks for fragment size (in Mb) (version 1 only)
-c cachesize
Set cache size (version 2 only)
-v ver
Use format version (1|2, 2 is default)

 

EXAMPLE


 famap -tN -b genome.famap org/chr_*.fa


 fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap


 re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200

See famap(1) and re-pcr(1)

 

SEE ALSO

/usr/share/doc/ncbi-epcr/README.txt

bioperl(1), e-pcr(1), famap(1) and re-pcr(1)

 

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.


 

Index

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
build-options:
EXAMPLE
SEE ALSO
AUTHORS

This document was created by man2html, using the manual pages.
Time: 21:12:44 GMT, April 16, 2011