VelvetOptimiser

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Description

The VelvetOptimiser is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. It searches a supplied hash value range for the optimum, estimates the expected coverage and then searches for the optimum coverage cutoff. It uses Velvet's internal mechanism for estimating insert lengths for paired end libraries. It can optimise the assemblies by either the default optimisation condition or by a user supplied one. It outputs the results to a subdirectory and records all its operations in a logfile.

Licence

GNU GPL 2

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 velvetopt and load default version of velvetopt as

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


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

module avail velvetopt

and choose explicit version you want to use.

VelvetOptimiser.pl -help

Documentation

https://github.com/tseemann/VelvetOptimiser/blob/master/README

Homepage

https://github.com/tseemann/VelvetOptimiser