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