Strain-level abundance analysis tool for short-read metagenomics
Strainify is an accurate strain-level abundance analysis tool for short-read metagenomics. It uses whole-genome alignments (Parsnp) to identify variant sites, maps metagenomic reads to a reference, and estimates strain abundances via a maximum likelihood model. It is designed to perform well on complex microbial communities and at low sequencing depths, where strain-resolved signal is sparse and closely related strains are easily confused.
