Related tools

Related tools

genome_comparator is a quick way to get distances, trees and an overview of a set of genomes. Depending on the question, these tools may be a better fit or a good complement:

Question	Tool	Notes
Trees from Mash distances	mashtree	Similar approach; NJ trees, with a bootstrap script
Accurate ANI values	skani, FastANI	More precise than Mash distances, especially for distant genomes
Remove redundant genomes	dRep	Dereplication with Mash, then ANI
Search large databases, metagenomes	sourmash	FracMinHash sketches; search, compare and taxonomic classification
Strain clusters for surveillance	PopPUNK	Clusters bacterial genomes using core and accessory distances
Taxonomic classification	GTDB-Tk	Places genomes in the GTDB taxonomy
Outbreak resolution (few SNPs)	Snippy, vSNP	SNP-level comparison against a reference
Distance matrix to tree, very large datasets	rapidNJ, FastME	Use with genome-comparator --phylip

When to use genome_comparator

• A fast first look at hundreds or thousands of genomes: structure, clusters and outliers.
• Checking species identity and spotting mislabelled or contaminated samples before a detailed analysis.
• Mixed inputs: assemblies and raw reads in the same run.
• Interactive exploration of the results with metadata (PCoA).

For the limits of Mash distances, see How it works.