Benchmarking strain-level profiling of Escherichia coli in short-read gut metagenomes (opens in new tab)

Metagenomes offer the potential to characterise Escherichia coli strain-level diversity within the human gut microbiome, informing our understanding of colonisation diversity and the genetic features distinguishing infection from carriage. Among numerous reference-based tools for short-read metagenomic strain-level profiling, the best approach remains unclear. Here, we benchmarked six published tools--PanTax, PathoScope, StrainGE, Strainify, StrainR2 and StrainScan--for their ability to detec...