lasvphylo

A pipeline for rapid phylogenetic analysis of Lassa virus (LASV) sequences

Lasvphylo is a specialized bioinformatics pipeline designed for rapid phylogenetic analysis of Lassa virus (LASV) sequences. This Nextflow-based pipeline enables researchers to quickly generate high-quality alignments and maximum likelihood phylogenetic trees from newly sequenced LASV samples.

I created lasvphylo to address our needs to quickly identify the phylogenetic relationships of newly identified strains in various regions of west-Africa. Initially the analyses took close to half a day, which now can be done within an hour.

The pipeline implements a streamlined five-step workflow specifically optimized for LASV analysis:

1. Gene orientation and isolation
2. Gene concatenation
3. Constrained phylogenetic inference

The complete source code, documentation, and example datasets are available on GitHub at Joon-Klaps/lasvphylo.