PB-metagenomics-tools

Welcome! Here you can find a variety of tools and pipelines tailored to using PacBio HiFi Reads for metagenomics. In addition to the resources currently available, we will continue to add new tools as they are developed.

Available tools and pipelines

Genome-Binning-Pipeline: Perform genome binning and MAG assessment on HiFi metagenomic assemblies with a streamlined workflow. Includes steps with minimap2, MetaBAT2, CheckM, and GTDB-Tk. Outputs high-quality MAG sequences and associated metadata.
Taxonomic-Functional-Profiling-Protein: Align HiFi reads to a protein database using DIAMOND and prepare inputs for MEGAN6, for the purpose of taxonomic and functional profiling. Provides access to taxonomic analyses (NCBI and GTDB), and allows functional analyses based on annotations from several databases (EC, SEED, InterPro2GO, eggNOG).
Taxonomic-Profiling-Nucleotide: Align HiFi reads to a nucleotide database using minimap2 and prepare inputs for MEGAN6, for the purpose of taxonomic profiling. This only provides access to NCBI taxonomic analysis, but may give higher resolution than with protein alignments. The GTDB taxonomy and functional annotations are not accessible downstream.
MEGAN-RMA-Summary: Obtain functional and taxonomic class count summaries for a set of RMA files created from the above MEGAN6 pipelines. Outputs absolute read counts and normalized read counts across samples for classes of each database, and summarizes the proportion of HiFi reads receiving functional and taxonomic annotations. Workflows are available for both protein-based RMA files and for nucleotide-based RMA files.

Each of these pipelines can be found in their respective folders. They are made available as Snakemake workflows. Snakemake is a python-based workflow manager. Snakemake workflows are highly portable because dependencies and environments are automatically setup using Anaconda/Conda. Snakemake also allows reproducibility, checkpointing, and the ability to scale workflows using HPC and cloud environments. Snakemake v5+ is required, and the workflows have been tested using v5.19+.

Documentation

All available documentation can be found in the docs/ folder above.

Currently available documentation:

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