Quast

Introduction

Quast is a software package that assesses genome assemblies. It is developed by the group that develops SPAdes.

Usage

To load:

module load quast

Quast is installed in the default python installation, so technically, thsi module laod directive is not required. However, it is useful because it loads other modules.

An example run:

quast.py test_data/contigs_1.fasta test_data/contigs_2.fasta -R test_data/reference.fasta.gz -G test_data/genes.gff

Installation Notes

Quast does not envisage installation into a non-standard directory.

Its setup.py script is highly customised and does not accept the usual --prefix= and --install-scripts options. The key to installing it in a non-standard location is inserting the right python executable at the head of the setup.py scritp of the quaast source distribution. I.e for marvin, thsi would be:

#!/usr/bin/env python2.7