Rapid species-level metagenome profiling and containment estimation with sylph
Technology tamfitronics MainShotgun metagenomics, the sequencing of all microbial genomes in a sample, has allowed for unprecedented insight into microbial communities without the need for cultivating those communities in a wet lab1,2. Computational analyses often proceed by assembling metagenome-assembled genomes (MAGs) or profiling the reads against a database of reference sequences. While assembly is necessary for novel genome discovery, a fundamental drawback is that assembly may not work for low-abundance organisms. Reference-based profiling methods instead leverage vast collections of microbial genomes3,4 to identify microorganisms and their abundances even for low-abundance organisms.Metagenomes can be complex and large5,6,7. This necessitates accurate profiling methods that scale with high-depth samples and big databases. Algorithmic paradigms that have emerged under...
