ToRQuEMaDA

ToRQuEMaDA performs dereplication of prokaryotic genomes by downloading, storing, and generating lists of representative genomes using alignment-free k-mer comparison for high-level taxonomic analyses.

Key Features:

• Alignment-free k-mer comparison: Employs word-based k-mer methods to compare and cluster genomes without sequence alignment.
• Iterative single-linkage clustering: Groups similar genomes using an iterative single-linkage clustering strategy based on k-mer composition.
• Divide-and-conquer processing: Breaks large datasets into subsets, processes them individually, and combines results to handle extensive genomic data.
• Parameter and heuristic evaluation: Assesses the influence of parameters and heuristics on clustering outcomes to optimize dereplication at high taxonomic levels.

Scientific Applications:

• High-level taxonomic dereplication: Optimized for dereplicating prokaryotic genomes at phylum and class taxonomic levels.
• Complementary clustering to other tools: Provides high-level clustering that complements dRep and Assembly-Dereplicator, which target lower taxonomic resolutions.

Methodology:

Performs word-based alignment-free k-mer comparison, iterative single-linkage clustering, a divide-and-conquer processing strategy, downloads and stores genomes, generates lists of representative genomes, and evaluates parameters and heuristics affecting clustering outcomes.