metabinR

metabinR performs abundance and compositional based binning on metagenomic samples directly from FASTA or FASTQ files.

Key Features:

• Direct File Processing: Operates directly on input FASTA or FASTQ files without requiring intermediate conversion steps.
• Java Backend with R Interface: Core functions are implemented in Java and called via rJava for computational efficiency.
• Parallel Implementation: Supports parallel processing for fast execution on metagenomic datasets.
• Flexible Input Handling: Accepts file paths or Biostrings/ShortRead sequence objects as input.
• Structured Output: Returns results as a MetabinResult S4 object containing cluster assignments, algorithm parameters, and input metadata.

Scientific Applications:

• Metagenomic Binning: Groups metagenomic sequences into bins based on abundance and compositional features for downstream taxonomic or functional analysis.

Methodology:

Abundance and compositional based binning algorithms implemented in Java and executed via rJava with parallel processing support.