Discover our collection of 4 research tools and applications for epidemiology.
Found 4 of 4 tools
Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). The method uses lineage-determining mutational "barcodes" derived from the UShER global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem.
LYVE version of the Snp Extraction Tool (SET), a method of using hqSNPs to create a phylogeny.
MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies The MOB-suite depends on a series of databases which are too large to be hosted in git-hub. They can be downloaded or updated by running mob_init or if running any of the tools for the first time, the databases will download and initialize automatically if you do not specify an alternate database location.
mlst is a command-line tool that scans contig files against PubMLST typing schemes to perform in silico multi-locus sequence typing (MLST), enabling rapid identification and typing of bacterial isolates.