fahash(1) sequence hash builder for reverse e-PCR


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]


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.


-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'


-w wordsize
Set word size when building hash tables
-f period
Set discontiguity when building hash tables
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)


 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)


This manual page was written by Andreas Tille <[email protected]> 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.