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dnaindex - index dna file for use with ANFO


dnaindex [ option ... ]


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


-V, --version
Print version number and exit.

-o file, --output file
Write output to file. file customarily ends in .idx. Default is

-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

-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.


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


Colon separated list of directories searched for genome files.

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