Skip to content

QUAST

QUality ASsessment Tool for Genome Assemblies (QUAST) evaluates genomes from multiple assemblies for comparison.

Installation

QUAST can be installed from the Bioconda Anaconda channel by loading the Miniforge module and then creating a Conda environment and installing QUAST into it (output below truncated):

$ module load miniforge
$ mamba create --quiet --yes --name quast_env
$ mamba activate quast_env
(quast_env) $ mamba install bioconda::quast

Looking for: ['bioconda::quast']
...
  Updating specs:
   - bioconda::quast
...
Confirm changes: [Y/n] Y
...
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Usage

To run QUAST, simply load the miniforge module and activate the Conda environment you previously created (see above for details):

$ module load miniforge
$ mamba activate quast_env
(quast_env) $ quast --help
QUAST: Quality Assessment Tool for Genome Assemblies
Version: X.Y.Z

Usage: quast [options] <files_with_contigs>

Options:
-o  --output-dir  <dirname>       Directory to store all result files
-r                <filename>      Reference genome file
-g  --features [type:]<filename>  File with genomic feature coordinates in the
                                  reference (GFF, BED, NCBI or TXT). Optional
                                  'type' can be specified for extracting only a
                                  specific feature type from GFF
-m  --min-contig  <int>           Lower threshold for contig length
-t  --threads     <int>           Maximum number of threads

For usage documentation, run quast --help.

GeneMark Licensing

An individual, free academic license is required if using GeneMark; QUAST will produce a warning message if GeneMark functionality is used without obtaining a license from here beforehand. Please select the GeneMarkS and LINUX 64 options and complete the remaining of the form with your personal details.

Example job

Serial job

Here is an example job running on 1 core and 1GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load miniforge
mamba activate quast_env

quast -r reference.fasta.gz \
      -g genes.gff \
      -t ${NSLOTS} \
      testcontigs_1.fasta \
      testcontigs_2.fasta

References