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

# dnaindex(1)

index dna file for use with ANFO

## NAME

dnaindex - index dna file for use with ANFO

## SYNOPSIS

**dnaindex \[** *option* **... \]**

## DESCRIPTION

**dnaindex** builds an index for a dna file.  Dna files must be indexed to be useable with  [**anfo**(1)](/anfo/1.md), it is possible to have multiple indices for the same dna file.

## OPTIONS

- \-V, --version

  Print version number and exit.

- \-o file, --output file

  Write output to  *file*. *file* customarily ends in  *.idx*. Default is  *genomename\_wordsize.idx*.

- \-g file, --genome file

  Read the genome from *file*. This file name is also stored in the resulting index so it can be found automatically whenever the index is used.  It is therefore best if *file* is just a file name without path.

- \-G dir, --genome-dir dir

  Add *dir* to the genome search path.  This is useful if the genome to be indexed is not yet in the place where it will later be used.

- \-d text, --description text

  Add *text* as description to the index.  This is purely informative.

- \-s size, --wordsize size

  Set the wordsize to *size*. A smaller wordsize increases precision at the expense of higher computational investment.  The default is 12, which with a stride of 8 yields a good compromise.

- \-S num, --stride num

  Set the stride to *num*. Only one out of  *num* possible words of dna is actually indexed.  A smaller stride increases precicion at the expense of a bigger index.  The default is 8, which in conjunction with a wordsize of 12 yields a good compromise.

- \-l lim, --limit lim

  Prevents the indexing of words that occur more often than *lim* times.  This can be used to ignore repetitive seeds and save the space to store them.  A good default depends on the size of the genome being indexed, something like 500 works for the human genome with wordsize 12 and stride 8.

- \-h, --histogram

  Produce a histogram of word frequencies.  This can be used to get an indea how the frequency distribution to select an appropriate value for  *--limit*.

- \-v, --verbose

  Print a progress indicator during operation.

## NOTES

**dnaindex** is limited to genomes no longer than 4 gigabases due to its use of 32 bit indices.  The index is quite large, so depending on parameters, a 64 bit platform is needed for genomes in the gigabase range.

If a genome contains IUPAC ambiguity codes, the affected seeds need to be expanded.  If there are many ambiguity codes in a small region, that results in an unacceptably large index.

## ENVIRONMENT

- ANFO\_PATH

  Colon separated list of directories searched for genome files.

## FILES

*/etc/popt*

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