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A gene-level metagenomics oriented pipeline for the analysis of shotgun (WGS) reads from microbial communities.

This pipeline is implemented using the open-source workflow management system Nextflow. This workflow management system is intended to run software seamlessly on local computer resources (via docker), on private HPC clusters (using singularity), or on public clouds (e.g. AWS batch).

See the Wiki for help getting started as well as advanced options


This work was supported by funding sources which include:

  • NIH NIGMS R35 GM133420 (PI: Amy Willis, Ph.D.)