Introduction

Here, we will walk through the translation of a pipeline for analysing the global source-sink dynamics of variants of concern (‘vocpl’). The original analysis is available as a NEXTFLOW pipeline joetsui1994/vocpl, though no NEXTFLOW knowledge is required to complete this walkthrough.

Note

In order to run the tutorial you will require access to beta.fasta, available under controlled access through GISAID.

Briefly, the vocpl workflow consists of the following steps:

1. Subsample alignment

2. Genome alignment (nextalign)

3. Maximum Likelihood Tree estimation

4. Sequence reconstruction (treetime)

5. Discrete trait analysis

vocpl workflow

We will walk through the first few steps of this pipeline in detail, and then provide links to the remaining modules for you to view/edit, and to allow the pipeline to be completed.