Strainy¶

Description¶

Strainy is a tool for phasing and assembly of bacterial strains from long-read sequencing data (either Oxford Nanopore or PacBio). Given a reference (or collapsed de novo assembly) and set of aligned reads as input, Strainy produces multi-allelic phasing, individual strain haplotypes and strain-specific variant calls. Compared to the current metagenomic strain profiling approaches, Strainy offers multiple unique features. First, it provides direct phasing of strains-specific variants, enabling evolutionary analysis of haplotypes rather than individual mutations. Second, Strainy provides a method to quantity strains and distinguish the most abundant and/or most divergent strains. Third, Strainy enables assembly-based analysis, which is useful in the absence of a high quality reference genome, especially in cross-samples comparison.

Environment Modules¶

Run module spider strainy to find out what environment modules are available for this application.

Environment Variables¶

HPC_STRAINY_DIR - installation directory
HPC_STRAINY_BIN - executable directory

Categories¶

biology, genomics, assembly