bionic (1) fahash.1.gz

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.