Quake

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Description

Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads. Quake adopts the k-mer error correction framework, first introduced by the EULER genome assembly package. Unlike EULER and similar progams, Quake utilizes a robust mixture model of erroneous and genuine k-mer distributions to determine where errors are located. Then Quake uses read quality values and learns the nucleotide to nucleotide error rates to determine what types of errors are most likely. This leads to more corrections and greater accuracy, especially with respect to avoiding mis-corrections, which create false sequence unsimilar to anything in the original genome sequence from which the read was taken.

License

Perl Artistic License

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of quake and load default version of quake as

module avail quake/ # list available modules
module load quake   # load (default) module


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail quake

and choose explicit version you want to use.

Documentation

Documentation is available at http://www.cbcb.umd.edu/software/quake/manual.html.

Homepage

http://www.cbcb.umd.edu/software/quake/index.html