Tutorials

Simple distance estimation

Download example E. coli genomes:

genome1.fna

genome2.fna

Run:

mash dist genome1.fna genome2.fna

The results are tab delimited lists of Reference-ID, Query-ID, Mash-distance, P-value, and Matching-hashes:

genome1.fna   genome2.fna     0.0222766       0       456/1000

Saving time by sketching first

mash sketch genome1.fna
mash sketch genome2.fna
mash dist genome1.fna.msh genome2.fna.msh

Pairwise comparisons with compound sketch files

Download additional example E. coli genome:

genome3.fna

Sketch the first two genomes to create a combined archive, use mash info to verify its contents, and estimate pairwise distances:

mash sketch -o reference genome1.fna genome2.fna
mash info reference.msh
mash dist reference.msh genome3.fna

This will estimate the distance from each query (which there is one of) to each reference (which there are two of in the sketch file):

genome1.fna   genome3.fna     0       0       1000/1000
genome2.fna   genome3.fna     0.0222766       0       456/1000

Querying read sets against an existing RefSeq sketch

Download the pre-sketched RefSeq archive:

refseq.msh

Sketch the reads (not provided here; >10x coverage of a single bacterial genome with any sequencing technology should work), using -u to improve results by filtering unique k-mers:

mash sketch -u reads.fastq

Run mash dist with the RefSeq archive as the reference and the read sketch as the query:

mash dist refseq.msh reads.fastq.msh > distances.tab

Sort the results to see the top hits and their p-values:

sort -gk3 distances.tab | head