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.

Availability

version 2.2.5

Use

module add velvetopt-2.2.5
VelvetOptimiser.pl -help

This makes available the path to the program binaries.

Documentation

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

Licence

GNU GPL 2

Program manager

meta@cesnet.cz

Homepage

https://github.com/tseemann/VelvetOptimiser