SEECER

From MetaCentrum
Jump to navigation Jump to search

Description

SEECER is a sequencing error correction algorithm for RNA-seq data sets. It takes the raw read sequences produced by a next generation sequencing platform like machines from Illumina or Roche. SEECER removes mismatch and indel errors from the raw reads and significantly improves downstream analysis of the data. Especially if the RNA-Seq data is used to produce a de novo transcriptome assembly, running SEECER can have tremendous impact on the quality of the assembly.

License

GNU GPL 3

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 seecer and load default version of seecer as

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


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

module avail seecer

and choose explicit version you want to use.

Documentation

http://sb.cs.cmu.edu/seecer/downloads/manual.pdf

Homepage

http://sb.cs.cmu.edu/seecer