README.md

genotype-fingerprints

Software for creating and comparing genotype fingerprints.
More information and datasets: http://db.systemsbiology.net/gestalt/genotype_fingerprints/
Preprint: https://doi.org/10.1101/208025

1. To create a fingerprint for a genome:
   bin/computeGF.pl myGenome path-to-my-genotypes/myGenome.gz
   ...will generate myGenome.outn.gz (and some other files)

2. To compare two fingerprints:
   bin/compareGFs.pl myFirstGenome.outn.gz mySecondGenome.outn.gz

3. To serialize fingerprints into a database, using L=1000:
   bin/serializeGFs.pl myFingerprintCollection 1000 @myListOfFingerprints
   bin/serializeGFs.pl myFingerprintCollection 1000 *.outn.gz

4. To compare a fingerprint to a database:
   bin/searchGFs.pl myGenome.outn.gz myFingerprintCollection
   ...see the data directory for an example database (Corpas family)

5. To compare two databases:
   bin/searchGFs.pl aFingerprintCollection anotherFingerprintCollection

6. To perform all-against-all comparisons in one database:
   bin/searchGFs.pl aFingerprintCollection

This project is related to (but distinct from) the Genome Fingerprints: https://github.com/gglusman/genome-fingerprints/