skDER

skDER enables microbial genome dereplication based on Average Nucleotide Identity (ANI) inference to select representative genomes for comparative genomic investigations.

Key Features:

• ANI-based dereplication: Dereplicates thousands of microbial genomes leveraging recent advances in average nucleotide identity (ANI) inference.
• Strict adherence to user-defined cutoffs: Achieves comparable pangenome coverage while strictly adhering to user-defined cutoffs for both ANI and aligned fraction (AF).
• Auxiliary parameter testing: Supports testing the number of representative genomes resulting from applying various clustering parameters.
• Automated genome downloading: Enables automated downloading of genomes belonging to a bacterial species or genus.
• Non-representative genome clustering: Clusters non-representative genomes to their closest representative genomes.
• Plasmid and phage filtering: Filters plasmids and phages prior to dereplication.

Scientific Applications:

• Comparative genomics: Selects representative genomes for fundamental comparative genomic investigations to determine major gain and loss events shaping the pangenome of a species or broader taxon.
• Computational burden reduction: Reduces computational burden by avoiding inclusion of all available genomes in studies where complete representation is unnecessary.
• Sampling bias minimization: Minimizes undesired effects on evolutionary analyses caused by over-representation of specific lineages due to sampling and sequencing bias.

Methodology:

skDER performs nucleotide-based genomic dereplication using ANI inference.