a fast replacement for MUMmer
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Readme.md

TUMmer

TUMmer is a drop-in replacement for MUMmer, being ten times faster on whole genomes. It is based on an enhanced suffix array instead of a suffix array. This makes it much faster, but also requires more memory. The detection of MUMs is limited to MUM candidates, i.e. matches which are only unique in the subject. Furthermore, TUMmer does not find all MUMs which overlap in the query. However, these only account for three percent of all MUMs and thus should not affect your analysis.

Installation

Grab the latest stable release and unpack it. TUMmer has libdivsufsort as a recommended requirement. It can be installed via the package manager on common Linux systems. If you did get the source, not as a tarball, but straight from the git repository, you will also need the autotools.

Building is as easy as follows.

$ autoreconf -fi -Im4  # optional when building from tarball
$ ./configure
$ make
$ make install

Usage

TUMmer follows Unix calling conventions:

$ tummer foo.fasta
> AE005674
   1         1        57
  65        65       165
 244       226       166
 411       393       165
 577       559        28

The following options (some with the same functionality as in MUMmer) are supported:

-b Compute forward and revere complement matches; default: forward only
-j, --join Treat all sequences from one file as a single genome. This might render the position field of the output useless.
-l, --min-length <INT> Minimum length of a MUM; uses p-value by default
-p <FLOAT> Significance of a MUM; default: 0.05
-r Compute only reverse complement matches; default: forward only
-v, --verbose Prints additional information
-h, --help Display help and exit
--version Output version information

The options -l and -p are mutually exclusive. The later of the provided arguments is used.

Multi-threading

Multi-threading is currently not supported but can easily be implemented. I will do so, if there is demand for it.

License

Copyright © 2016 Fabian Klötzl kloetzl@evolbio.mpg.de
License GPLv3+: GNU GPL version 3 or later.

This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. The full license text is available at http://gnu.org/licenses/gpl.html.

Some files may be licensed differently.