---
name: "fahash"
section: "1"
platform: "linux"
package: "ncbi-epcr"
version: "2.3.12-1-10"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fahash"
---

# fahash(1)

sequence hash builder for reverse e-PCR

## 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)](/famap/1.md) and re-pcr(1)

## SEE ALSO

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

bioperl(1), e-pcr(1), [famap(1)](/famap/1.md) 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.