example.ncbi-assemblies

Building a sourmash database from NCBI assemblies

This directory contains a Makefile that will build a sourmash database for the genome in GCF_000018865.1_ASM1886v1_genomic.fna.gz and the proteome in GCF_000018865.1_ASM1886v1_protein.faa.gz

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

The Makefile does the following:

1. Build a summary of the genome and proteome files in the 'fromfile' format

The Makefile first uses the script ../genbank-to-fromfile.py to scan the genomes and produce a summary file, build.csv, that contains names and source genomes for sourmash signatures. (In this case, there's only one genome and one proteome, note!)

Names for the genomes are taken from the NCBI assembly_summary.txt file that is distributed with Refseq and Genbank assemblies.

2. Create the signatures using sourmash sketch

Next, the Makefile runs

sourmash sketch fromfile build.csv -p dna -p protein -o all.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, and -p protein tells sourmash to construct protein sketches, too.

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

Finished!

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