Difference between revisions of "Quast"
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= Introduction = | = Introduction = | ||
| − | Quast is a software package that assesses genome assemblies. It is developed by the group that develops SPAdes. | + | 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 = | = Usage = | ||
Revision as of 12:27, 10 February 2017
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
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
