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.
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
- 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.
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: