Sequence distances with sketchlib

Sketchlib is a tool for rapid sketching and distance estimation, which is available from https://github.com/bacpop/sketchlib.rust.

Sketchlib indexes are available from OSF here: https://osf.io/rceq5/overview.

For routine closest-genome searches, use the ATB command line tool. It installs sketchlib v0.2.4 when you run atb sketch install.

atb sketch install
atb sketch fetch
atb sketch query my_genome.fasta --knn 50

The CLI can also download the matching assemblies:

atb sketch query my_genome.fasta --knn 50 --download ./closest_genomes

The latest index, which is all assemblies up to and including incremental release 202505 (ie it is release 0.2 plus incremental releases 202408 and 202505), is in the files Aggregated/atb_sketchlib.aggregated.202505.skd and Aggregated/atb_sketchlib.aggregated.202505.skm. Older index files are also available.

The distributed indexes have sketch size 1024 with k=17.

Manual sketchlib use

The following commands are for power users who want to call sketchlib directly, for example to calculate distances within a subset.

To calculate distances of a subset of the data, use a command such as:

sketchlib dist -v -k 17 --subset Haemophilus_influenzae.txt --ani atb_sketchlib.aggregated.202505 --threads 4 > dists.txt

Where the --subset file contains the list of samples you want to include. Removing --ani will calculate Jaccard distances.

To query new samples against the index, first sketch it:

sketchlib sketch -v -o query -k 17 -f queries.tsv -s 1024

(where queries.tsv contains query samples with name and file location, tab separated)

Then query it

sketchlib dist -v -k 17 atb_sketchlib.aggregated.202505 query