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 = | ||
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module load quast | module load quast | ||
| − | Quast is installed in the default python installation, so technically | + | 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: | 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 | quast.py test_data/contigs_1.fasta test_data/contigs_2.fasta -R test_data/reference.fasta.gz -G test_data/genes.gff | ||
| + | |||
| + | <ins>Explanation</ins>: | ||
| + | * 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 = | = Installation Notes = | ||
Latest revision as of 17:30, 14 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
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
