This repository contains the scripts for reproducing the results of the following publication (from the ISMB 2024 HiTSeq Proceedings)

Harun Mustafa, Mikhail Karasikov, Nika Mansouri Ghiasi, Gunnar Rätsch, and André Kahles. "Label-guided seed-chain-extend alignment on annotated De Bruijn graphs." Bioinformatics 40, no. Supplement_1 (2024): i337-i346. DOI: 10.1093/bioinformatics/btae226

• MetaGraph (development commit bd39d9594e77f276e674033b52d9b26ec3a281e3, includes KMC)

• ART Illumina (v2.5.8)
• pbsim3 (commit v3.0.0)
• PacBio ccs (v6.4.0)

• bbmap (v38.86)
• samtools (experiments were run with v1.17)

• PLAST (commit 451369eb23e84328ff9334398d185798d2dc5149)
• GraphAligner (v1.0.17b)

• WGSUniFrac (commit d5c698ba4699aba168fd29fc00024d655c36183f, included here)
• numpy (v1.26.0)
• pandas (v.2.1.1)

• https://public.bmi.inf.ethz.ch/resources/mla/

1. To install most of the required software for the evaluation, set up a conda environment using the provided environment.yml file: conda env create -f environment.yml
2. Activate the environment: conda activate mla
3. Download the pre-compiled binaries of metagraph, PLAST, kmc, and parse_plast from here and place them in your working directory.
4. Download the genomes from here to a directory named references. A list of accessions is in accession_list
5. Download the random entropy source file seed2 (used to generate query sets)
6. Download the accession-ID augmented taxonomic tree from the augmented directory here

1. Simulate reads for each genome:

   for a in references/*.fa; do ./make_sample.sh $a; done
   for a in illumina hifi clr ont; do ./make_subset.sh $a; done
   

2. Build the MetaGraph, PLAST, and GFA indexes by running ./make_graph.sh. In this script, you can set the number of threads in the variable $NTHREADS. We provide precomputed indexes for MetaGraph here and for PLAST here.
3. Generate query reads by running ./make_subset.sh

for a in query_reads/*.fa; do
    ./map_query_sca.sh $a
    ./map_query_mla.sh $a
    ./map_query_plast.sh $a
    ./map_query_ga.sh $a
done

• To compile some of the software yourself from source
  • parse_plast.cpp: we have provided a Makefile.
  • PLAST: we have provided a template CMakeLists.txt file in plast_cmake. Please edit it to point to the include directory and static lib of Bifrost.
  • MetaGraph (with packaged kmc): follow the instructions here. Remember to checkout the commit listed above from the hm/aln_alt_label_change branch before compiling.
• Run metagraph align to view the help menu listing alignment parameters. To list a more advanced set of parameters, run metagraph align --advanced.