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

# anfo(1)

find best alignment of short reads to database

## NAME

anfo - find best alignment of short reads to database

## SYNOPSIS

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

## DESCRIPTION

**anfo** aligns (short) sequencing reads to a (gigabase sized) database.  It uses a heuristic seeding method, but then applies a genuine aligner that allows gaps, understands damage patterns in ancient dna and produces an easy to interpret score.

Input files can be any variety of FastA or FastQ files, or a native **anfo** binary file, optinally compressed using  **gzip**or**bzip2**. The file format is automatically recognized and other formats may be added.

## OPTIONS

- \-V, --version

  Print version number and exit.

- \-o file, --output file

  Write output to  *file*. *file* will be written in the native **anfo** binary format, which can be operated upon using **anfo-tool** or the bindings to **guile**.

- \-c conffile, --config conffile

  Read configuration from  *conffile*. This file configures which indices are used, and by extension to which genomes an alignment is made, what parameters to use in the aligner and can set paths.  See the example file.

- \-p num, --threads num

  Start *num* threads for alignment.  One such thread per processor core is usually best.

- \-x num, --ixthreads num

  Start  *num* threads for indexing.  Indexing normally uses less cpu power than alignment, so fewer indexers than aligners is normally best.

- \--solexa-scale

  When reading FastQ files, use the Solexa scale (log-odds-ratios) instead of the standard Phread scale (probabilities).  If you use Solexa/Illumina sequencers, refer to your documentation whether you need this.  Else you don't.

- \--fastq-origin ori

  Set origin for FastQ decoding to *ori*. The standard and default is 33, but it must be set to 64 for some versions of the Solexa/Illumina software.  If you use Solexa/Illumina sequencers, refer to your documentation whether you need this.  Else you don't.

- \-q, --quiet

  Suppress all output except fatal errors.

- \-v, --verbose

  Print a progress indicator during operation.

## ENVIRONMENT

- ANFO\_PATH

  Colon separated list of directories searched for genome and index files.

## FILES

*/etc/popt*

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

*~/.popt*

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

*/usr/share/doc/anfo/example/\*.cfg*

Example configuration files to be used with  **anfo**.

## BUGS

None known.

## AUTHOR

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

## SEE ALSO

http://bioinf.eva.mpg.de/anfo

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