niemasd/multivirusconsensus repository overview

⁠MultiVirusConsensus (MVC)

MultiVirusConsensus (MVC): Fast consensus genome reconstruction of multiple viruses from a mixed sample

⁠Installation

MVC is written in Python 3 and has the following dependencies:

• Minimap2⁠
• Samtools⁠
• ViralConsensus⁠

Once you have all dependencies installed, you can simply download MultiVirusConsensus.py⁠ to your machine and make it executable:

wget "https://github.com/niemasd/MultiVirusConsensus/releases/latest/download/MultiVirusConsensus.py"
chmod a+x MultiVirusConsensus.py
sudo mv MultiVirusConsensus.py /usr/local/bin/MultiVirusConsensus.py # optional step to install globally

We also provide a Docker image with all dependencies installed: niemasd/multivirusconsensus⁠

⁠Usage

A help message demonstrating MVC usage can be viewed using the -h/--help argument.

⁠Example

./MultiVirusConsensus.py -o output -i example/reads.illumina.30X.fq.gz -r example/NC_001802.fas example/NC_045512.fas example/NC_063383.fas -p example/NC_045512.bed

⁠Optional Arguments

While we anticipate that MVC should perform reasonably well using the default settings, some settings can be optionally tweaked as desired.

⁠Minimap2 Arguments

By default, we run Minimap2 using its short read preset (-x sr). To use a different present, or to manually specify Minimap2 mapping settings, you can provide the Minimap2 arguments you want to use via: --minimap2_args

For example, to use the accurate long reads preset (-x lr:hq), you could run the following:

./MultiVirusConsensus.py --minimap2_args '-x lr:hq' -i hq_long_reads.fq.gz -r example/NC_001802.fas example/NC_045512.fas example/NC_063383.fas -o output

In general, please only include arguments from the Indexing:, Mapping:, and Alignment: sections of the Minimap2 usage: do not include arguments from the Input/Output: section of the Minimap2 usage!

⁠ViralConsensus Arguments

By default, we run ViralConsensus using its default settings. To manually specify ViralConsenus settings, you can provide the ViralConsensus arguments you want to use via: --viral_consensus_args

For example, to change the minimum depth setting to 1 (-d 1), you could run the following:

./MultiVirusConsensus.py --viral_consensus_args '-d 1' -i example/reads.illumina.30X.fq.gz -r example/NC_001802.fas example/NC_045512.fas example/NC_063383.fas -o output

In general, please only include arguments related to consensus sequence calling: do not include arguments related to input/output files!

⁠Interpreting Results

⁠Visualizing Coverages

You can interactively visualize the coverages of each reference sequence of a MultiVirusConsensus run using our visualization web application⁠.

⁠Helper Scripts

We provide helper scripts for post-processing of MultiVirusConsensus results in the scripts⁠ directory in this repository. Notably, the summary.py⁠ script calculates many summary statistics about the read mapping, base/indel counting, and consensus sequence calling processes and outputs them as a TSV: most importantly, it also attempts to predict which viruses likely actually exist in the sample (e.g. for multi-virus surveillance panels).

⁠Citing MultiVirusConsensus (MVC)

If you use MVC in your work, please cite: