SYNOPSISdnaindex [ option ... ]
DESCRIPTIONdnaindex 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
customarily ends in
- -g file, --genome file
Read the genome from
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
is just a file name without path.
- -G dir, --genome-dir 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
as description to the index. This is purely informative.
- -s size, --wordsize size
Set the wordsize to
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
Only one out of
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
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
- -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 index.
Colon separated list of directories searched for genome files.
- The system wide configuration file for popt(3). dnaindex identifies itself as "dnaindex" to popt.
- Per user configuration file for popt(3).
AUTHORUdo Stenzel <[email protected]>