---
name: "fa2dna"
section: "1"
platform: "linux"
package: "anfo"
version: "0.98-8"
release: "Debian 11 (Bullseye)"
platforms: ["linux"]
url: "https://new.carta.tech/fa2dna"
---

# fa2dna(1)

format fasta database for use with ANFO

## NAME

fa2dna - format fasta database for use with ANFO

## SYNOPSIS

**fa2dna \[** *option* **\|** *file* **... \]**

## DESCRIPTION

**fa2dna** reads one or more files in fasta format and reformats them into a database suitable for  [**anfo**(1)](/anfo/1.md). The input file(s) can contain more than one sequence, and each sequence can be broken up into multiple contigs by a stretch of Ns.  All IUPAC ambiguity codes are fully supported.

## OPTIONS

- \-V, --version

  Print version number and exit.

- \-o file, --output file

  Write output to  *file*.*file* should end in  *.dna*, because  **anfo** and some downstream tools might stumble over a different extension.  Default is the genome name with the  *.dna* extension.

- \-m N, --maxn N

  Sets the maximum number of *N*s to be interpreted as IUPAC ambiguity codes to *N*; any longer stretch is interpreted as separing contigs.  Default is 2.

- \-g name, --genome name

  Sets the genome name to *name*. This name is stored in the output file and will be used by **anfo** to identify the matched genome in its output.  The genome should be a prefix of the output file name to allow downstream tools to find it. The name should be short, but unique, something like "hg18" or "pt2" for human or chimpanzee genomes would work fine.

- \-d text, --description text

  Adds *text* as description to the metadata.  This is purely informational.

- \-v, --verbose

  Causes a progress indicator to be printed.

## FILES

*/etc/popt*

The system wide configuration file for [**popt**(3)](/popt/3.md). **fa2dna** identifies itself as "fa2dna" to popt.

*~/.popt*

Per user configuration file for [**popt**(3)](/popt/3.md).

## BUGS

None known.

## AUTHOR

Udo Stenzel \<udo\_stenzel@eva.mpg.de\>

## SEE ALSO

[**anfo**(1)](/anfo/1.md), [**fa2dna**(1)](/fa2dna/1.md) [**popt**(3)](/popt/3.md), **fasta**(5)