example.private

Building a private sourmash database

This directory contains a Makefile that will build a private database for the 64 genomes used in Awad et al., 2017.

Run make to run the entire pipeline. (You'll need sourmash v4.4.0 installed.)

The Makefile does the following:

1. Download and unpack the genomes

The Makefile runs curl to download the genomes from the OSF project, and then unpacks them.

2. Build a summary of the genomes in the 'fromfile' format

Next, the Makefile uses the script ../fasta-to-fromfile.py to scan the genomes and produce a summary file, build.csv, that contains names and source genomes for sourmash signatures.

3. Create the signatures using sourmash sketch

Finally, the Makefile runs

sourmash sketch fromfile build.csv -p dna -o podar-ref.zip

to sketch all of the genomes in build.csv. The parameter string -p dna tells sourmash to construct DNA sketches using the default parameters; any number of parameter strings can be provided, one with each -p.

The names for the output signatures are taken from build.csv.

Finished!

You can run sourmash sig summarize podar-ref.zip to get a summary of the contents of the zip file, or sourmash sig describe podar-ref.zip to get a listing of all the signatures.