Quast

Introduction

Quast is a software package that assesses genome assemblies. It is developed by the group that develops SPAdes, so Pavel Pevsner's group at St. Petersburg State University.

Usage

To load:

module load quast

Quast is installed in the default python installation, so - technically - this "module load" directive is not required. However, it is useful because it loads other modules and so is recommended.

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

Explanation:

• the first two arguments are a pair of FASTA files. However these are not paired FASTQ reads, this must be an assembly which happens to be split in two.
• -R this is for the reference, however it is only optional. IF available, quast can issue more metrics, and without it, less.
• -G also the tool would like to see genes or features. However if there is no such file, quast can be run before hand as a gene finder. The option --gene-finding allows this.

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, this would be:

#!/usr/bin/env python2.7