ICoVeR

ICoVeR facilitates verification and refinement of metagenomic contig bins to improve draft microbial genome reconstruction from high-throughput sequencing datasets.

Key Features:

• Contig bin verification and refinement: Groups contigs into genome bins and supports refinement of draft microbial genomes from metagenomic assemblies.
• Visualization capabilities: Provides a parallel coordinates view and a dimensionality reduction plot to compare and visualize multiple binning outputs.
• Integration of automatic binning algorithms: Integrates results from MetaBAT, CONCOCT, and MyCC to support consensus-based curation of bin assignments.
• Evaluation metrics: Assesses bin quality using completeness and contamination metrics to quantify improvements after refinement.
• Benchmarking and demonstrated results: Applied to an anaerobic digestion metagenomic dataset (31 refined bins with 23 showing increased completeness and decreased contamination) and benchmarked on Sharon's infant gut metagenome.
• Targeting uncultivated microbes: Focuses on recovering genomes from previously uncultivated microbial taxa ("microbial dark matter") in high-throughput sequencing studies.
• Implementation: Implemented in R.

Scientific Applications:

• Metagenomic genome reconstruction: Refining contig-to-bin assignments to produce higher-quality draft genomes from metagenomic data.
• Microbial ecology and diversity studies: Improving genome recovery for analyses of microbial diversity, taxonomy, and function within ecosystems.
• Anaerobic digestion microbiome analysis: Refinement of genome bins from anaerobic digestion metagenomes to enhance reconstruction of community members.
• Infant gut microbiome benchmarking: Benchmarking and validation of bin refinement approaches using Sharon's infant gut metagenome.

Methodology:

Integrates outputs from MetaBAT, CONCOCT, and MyCC; visualizes binning results via parallel coordinates and dimensionality reduction plots; enables curation of contig-to-bin assignments; and evaluates changes in completeness and contamination for refinement and benchmarking.