SnakeMAGs

SnakeMAGs reconstructs prokaryotic genomes from Illumina metagenomic reads to enable genome-centric analysis of microbial communities.

Key Features:

• Input support: Processes Illumina sequencing metagenomic reads as input data.
• Read quality control: Performs read trimming and filtering using illumina-utils and Trimmomatic.
• Optional host removal: Removes host-derived reads using Bowtie2 when required.
• Assembly: Assembles metagenomic reads into contigs with MEGAHIT.
• Binning: Groups contigs into genome bins using MetaBAT2.
• Bin quality assessment: Assesses bin completeness and contamination with CheckM and screens with GUNC.
• Taxonomic classification: Classifies metagenome-assembled genomes using GTDB-Tk.
• Abundance estimation: Estimates relative abundances of MAGs using CoverM.
• Workflow management: Implements the pipeline using the Snakemake workflow management system.
• Scalability: Supports execution from single-core workstations to multicore clusters and grids.

Scientific Applications:

• Genome-centric microbial ecology: Reconstruction of metagenome-assembled genomes to enable analysis of microbial diversity and metabolic potential.
• Relative abundance profiling: Quantification of MAG abundances across metagenomic samples.
• Comparative benchmarking: Evaluation and comparison of MAG recovery and taxonomic breadth across workflows and datasets, e.g., termite gut metagenomes versus alternative pipelines.

Methodology:

Workflow steps explicitly include read quality control with illumina-utils and Trimmomatic, optional host read removal with Bowtie2, assembly with MEGAHIT, binning with MetaBAT2, bin quality assessment with CheckM and GUNC, taxonomic classification with GTDB-Tk, and abundance estimation with CoverM, all orchestrated via Snakemake.