QUAST is a popular bioinformatics software for genome assembly evaluation. This project aims to improve the legacy QUAST codebase and put the QUAST functionality on top of the Snakemake workflow management system to enable reproducible and scalable data analysis. This effort is funded by the CZI Award for Open Source Software Tools Essential to Biomedicine.
NB! This is a work-in-progress project, so expect many bugs. Also, not all legacy QUAST features are currently implemented. In partucular, metaQUAST is not working yet. For stable and fully-functional QUAST, please use our latest release or the online version.
You will need Mamba/Mambaforge (recommended) or Conda. If you already have Conda and want to switch to Mamba you can install it with
$ conda install -n base -c conda-forge mamba
Once you have one of them, it is very easy to install Snakemake (7.0.0 or higher) and other QUAST dependencies (specified in the env YAML files) by typing
$ mamba create -c conda-forge -c bioconda -n quast_sm snakemake python=3.9
$ mamba env update -n quast_sm --file envs/basic.yaml # all basic QUAST dependencies
$ mamba env update -n quast_sm --file envs/busco.yaml # if conservative gene finding (BUSCO) is also needed
Note:
- If you have Conda rather than Mamba, substitute
mambawithconda. NB! We experienced a problem with installing BUSCO viaconda. - Python 3.9 is needed since QUAST relies on pysam that is currently incompatible with Python 3.10 (as of 23.06.2022)
- You can use any other environment name instead of
quast_sm
Now just activate the environment and you are ready to go!
$ mamba activate quast_sm
Note: you may need to run mamba init and restart the shell to enable mamba activate for the first time; or simply use conda activate quast_sm.
To run QUAST on sample files from ./test_data/ type one of the following sample commands
$ ./quast.py -o quast_test_output_with_ref test_data/contigs_1.fasta test_data/contigs_2.fasta -t 4 -r test_data/reference.fasta -g gene:test_data/genes.gff -g operon:test_data/operons.bed # test with reference
$ ./quast.py -o quast_test_output_no_ref test_data/contigs_1.fasta test_data/contigs_2.fasta
You might find much more details on QUAST, its options and output in the online manual, main GitHub repo, and the project page at the CAB website.
If you want to report a bug or ask something, please use our issue trackers (this one specifically for Snakemake-based version or this one for general QUAST issues) or email us.