Introduction

VelvetOptimiser is designed to run as a wrapper script for the Velvet assembler (Zerbino and Birney 2008) and to assist with optimizing 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 optimize the assemblies by either the default optimization condition or by a user supplied one. It outputs the results to a subdirectory and records all its operations in a log file.

For more information, visit the VelvetOptimiser page at GitHub.

Programming language: Perl

Brief description: A wrapper script for the Velvet assembler, to assist with optimizing the assembly.

Open source license: GPL 2.0