Benchmarks for the Fulgor index
This repository contains benchmarking code and evaluation scripts for the Fulgor index.
- Snakefile - Rules for generating the simulated reads and evaluating pseudo-alignment output.
- sim_reads.sh - Script using mason to generate simulated reads.
- evaluate_mappings.py - Given the pseudo-alignment mappings output by Fulgor, generate the json file that contain the different mapping statistics.
- map_contigs.sh - Script mapping references to ids.
More scripts to be populated soon.
Packages
Mason - 2.0.9
Seqkit - 2.4.0