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FAHASH

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 AT debian DOT 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.

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