Fig. 1
From: Genomic surveillance of Rift Valley fever virus: from sequencing to lineage assignment
Schematic representation of the command line workflow. The workflow begins with virus classification using DIAMOND and reports the output as a text file with taxonomic information and similarity metrics. Phylogenetic analysis is performed using a default phylogenetic reference dataset generated by Neighbor-Joining (NJ), Maximum likelihood (ML) and Bayesian tree. Users can specify which phylogenetic reference dataset to use. Query sequences are aligned to the reference dataset multiple sequence alignment with MAFFT, and a ML phylogenetic tree is constructed followed by lineage assignment. An output file with the lineage assignment, bootstrap values and likelihood test ratio is generated in comma-separated values (CSV) file format