satta/speck-benchmarks

Benchmarking scripts for speck

Benchmark scripts for Speck annotation checker

gal_test.pl -- GAL/Bioperl variant

• Requires GAL (http://www.sequenceontology.org/software/GAL.html) and Bioperl (from CPAN)

gffutils_test.py -- gffutils/Biopython variant

• Requires gffutils (https://pythonhosted.org/gffutils) and Biopython (both installable via pip)
• Python3 compatible

specs directory

• contains use cases

Usage

docker run -v /tmp:/mnt/out satta/speck-benchmarks /opt/scripts/run_performance_checks.sh /opt/genomes /mnt/out /opt/scripts