aaKomp

Description

Assess draft genome completeness using a fast, alignment-free, k-mer hash-based approach (aaKomp). This tool uses amino acid k-mers and a multi-index Bloom filter (miBf) to estimate the completeness of genome assemblies.

Credits

Concept: Johnathan Wong and Rene L. Warren
Design and Implementation: Johnathan Wong

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Installing from Conda (Preferred method)

Under construction

Installing from Source

Clone from GitHub

git clone https://github.com/bcgsc/aakomp.git
cd aakomp
meson --prefix /path/to/install build
cd build
ninja install

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Dependencies

• GCC 7+ with OpenMP
• Python 3.9+
• zlib
• meson
• ninja
• tcmalloc
• sdsl-lite
• libdivsufsort
• btllib
• libsequence
• gperftools
• numpy
• matplotlib

Installing Dependencies with Conda

We recommend creating a fresh conda environment:

conda create --name aakomp
conda activate aakomp
conda install -c conda-forge -c bioconda --file requirements.txt

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Running aaKomp

You can run aaKomp either directly or using the wrapper script run-aakomp.

Wrapper Script: run-aakomp

The run-aakomp wrapper automates:

• Checking for existing miBF
• Building a miBF if missing using make_mibf
• Running aakomp
• Running post-analysis with aakomp_score.py

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Demo Example

This demo runs aaKomp on the C. elegans genome using the nematoda_odb12 ortholog protein set.

# Download the C. elegans genome
wget -nc https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/985/GCF_000002985.6_WBcel235/GCF_000002985.6_WBcel235_genomic.fna.gz

# Decompress the genome
gunzip -c GCF_000002985.6_WBcel235_genomic.fna.gz > GCF_000002985.6_WBcel235_genomic.fna

# Link the protein reference file to the current directory (assumes you have nematoda_odb12 in the current directory)
ln -sf nematoda_odb12/nematoda_odb12.faa ./

# Run aaKomp through the wrapper
run-aakomp --db-dir ./ \
  --reference nematoda_odb12.faa \
  --input GCF_000002985.6_WBcel235_genomic.fna \
  -o demo

Command-line Options

run-aakomp options (partial list):

Option	Description
--input -i	Genome file (FASTA) to assess
--reference -r	Protein database (FASTA, amino acid)
--output -o	Output prefix
--db-dir	Directory to store miBF database
--threads -t	Number of threads (default: 48)
--hash -H	Number of hash functions for miBF (default: 9)
--kmer -k	Amino acid k-mer size (default: 9)
--lower_bound -l	Minimum occupancy threshold (default: 0.7)
--rescue_kmer	Number of consecutive k-mers to initiate a seed
--max_offset	Max distance to extend seed during chaining
--track-time	Track runtime of each major step
--dry-run	Print commands only, do not execute
--verbose -v	Verbose output
--debug	Debug mode for internal troubleshooting

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License

aaKomp Copyright (c) 2025
British Columbia Cancer Agency Branch. All rights reserved.

Licensed under the GNU General Public License v3. See LICENSE or http://www.gnu.org/licenses/.

For commercial licensing inquiries, contact:
Patrick Rebstein – [email protected]