Viralmsa
Description
ViralMSA is a tool to perform reference-guided multiple sequence alignment of viral genomes. ViralMSA wraps around existing read mapping tools such as Minimap2, and as such, it can natively improve as methods of read mapping evolve. Importantly, this approach scales linearly with the number of sequences and can be massively parallelized. However, insertions with respect to the reference genome will be thrown away. This is fair for many viral analyses (e.g. phylogenetic inference, as insertions with respect to the reference likely lack phylogenetic information), but it may not be appropriate for all contexts.
Environment Modules
Run module spider viralmsa to find out what environment modules are available for this application.
System Variables
- HPC_VIRALMSA_DIR - installation directory
- HPC_VIRALMSA_BIN - executable directory
- HPC_VIRALMSA_EXE - example directory
Citation
If you publish research that uses viralmsa you have to cite it as follows: