The nf-core viralrecon pipeline

nf-core/viralrecon is a Nextflow-based analysis pipeline used to perform assembly and intra-host/low-frequency variant calling for viral samples and supports both Illumina and Nanopore sequencing data

For Illumina short-reads the pipeline is able to analyse metagenomics data typically obtained from shotgun sequencing (e.g. directly from clinical samples) and enrichment-based library preparation methods (e.g. amplicon-based: ARTIC SARS-CoV-2 enrichment protocol; or probe-capture-based). An outline of the workflow is shown in the following figure:

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Briefly, the sequence data is quality controlled (QC) then, depending on the type of data and what analyses you’d like to perform, the sequence reads are either mapped to a reference and variant calling performed or else the data is de novo assembled. Alternatively, like most nf-core pipelines, you can do both.

Regardless of which assembly type you require, downstream analyses such as lineage assignment and QC of the assembly are then performed before the results are summarised using MultiQC. As with all nf-core pipelines and all bioinformatics tools in fact, it’s always worth reading the documentation to understand the different steps of the pipeline and what other options there may be available.

Note: We are using viralrecon and viral genomes as the files are small and the analysis quicker to run. It is not our aim to specifically focus on viral genomics but rather use viralrecon as an example of an existing pipeline that you can easily modify and run.