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seqSight is a tool to jointly profile microbial strains, genes, and biosynthetic gene clusters from metagenomics data; it is designed to provide maximum utility to the user by incorporating a number of analysis modules for the quantification of not only bacterial strains but also gene families and biosynthetic gene clusters. seqSight also incorporates quality control modules and visualization tools.

seqSight Documentation

You could find the seqSight manual here.