Build and query Metagraph indexes

This repository contains a (snakemake) workflow to build Metagraph indexes and bash scripts to run queries against the indexes that have been used for the experiments in this paper https://doi.org/10.1101/2023.07.21.550101.

Dependencies

• snakemake v7.30 (recommended installation via conda);
• metagraph, commit 5c2a12b.

Usage

snakemake --cores all --configfile <config.yml> -- <rule>

Rules to produce various annotations:

• row_diff
• row_diff_flat
• row_diff_sparse
• row_diff_brwt
• relax_brwt_arity

For example:

snakemake --cores 48 --configfile se-150k.yml -- relax_brwt_arity

Note: building any of the variants produces the "plain" variant that is not row-diff compressed.

Extracting build times

Use provided python script to sum build times for metagraph variants:

python gather_build_times.py <path_to_log_dir> <mode>

Logs are written to <output-dir>/<exp-name>/logs.

Config file specification

• outputs are written to <output-dir>/<exp-name> with output-dir defaulting to output/<exp-name> if not specified.
• file containing list of filepaths is specified with input-file-lists
• path to metagraph-bin metagraph binary must be supplied.
• Number of cores used set to threads where possible.

See the file example-config.yml for an example.

Run queries

See the examples provided in the scripts high_hit_queries.sh and low_hit_queries.sh.