| FAHASH(1) | User Commands | FAHASH(1) |
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.
| April 2008 | Reverse e-PCR: sequence hash builder version 2.3.9 |