UShER¶
UShER is a program that rapidly places new samples onto an existing phylogeny using maximum parsimony. It is particularly helpful in understanding the relationships of newly sequenced SARS-CoV-2 genomes with each other and with previously sequenced genomes in a global phylogeny. This has emerged as an important challenge during this pandemic for enabling genomic contact tracing since the viral phylogeny is already very large (>100K sequences, see https://github.com/roblanf/sarscov2phylo/releases) and is expected to grow by many fold in the coming months.
Environment Modules¶
Run module spider UShER to find out what environment modules are available for this application.
System Variables¶
- HPC_USHER_DIR - installation directory
- HPC_USHER_BIN - executable directory