omixplatform / genome-fingerprints

Software for creating and comparing genome fingerprints.

genome-fingerprints

Software for creating and comparing genome fingerprints.
More information and datasets: http://db.systemsbiology.net/gestalt/genome_fingerprints/
Preprint: http://www.biorxiv.org/content/early/2017/06/27/130807

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

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

3. To serialize fingerprints into a database, using L=120:
   bin/serializeDMFs.pl myFingerprintCollection 120 @myListOfFingerprints
   bin/serializeDMFs.pl myFingerprintCollection 120 *.outn.gz

4. To compare a fingerprint to a database:
   bin/searchDMFs.pl myGenome.outn.gz myFingerprintCollection
   ...see the data directory for an example database (CEPH1463 pedigree)

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

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

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