Hifi assembly

MetaMDBG is a fast and memory-efficient assembler designed for long and accurate metagenomics reads (e.g. PacBio HiFi, Nanopore R10). It is optimized for metagenomes, but also works well on bacterial isolates samples. Up-to-date benchmarks are provided in the Results section below.

The method nanoMDBG for assembling Nanopore R10 simplex reads is integrated in metaMDBG.

Developper: Gaëtan Benoit
Contact: gaetanbenoitdev at gmail dot com

News

May 2026: MetaMDBG v1.4 is out!

• Major performance update (both runtime and memory)
• Better polishing

Check out the new results below.

Installation

Conda

conda install -c conda-forge -c bioconda metamdbg

Building from source (using conda)

# Download metaMDBG repository  
git clone https://github.com/GaetanBenoitDev/metaMDBG.git

# Create metaMDBG conda environment
cd metaMDBG
conda env create -f conda_env.yml
conda activate metamdbg1.4
conda env config vars set CPATH=${CONDA_PREFIX}/include:${CPATH}
conda deactivate

# Activate metaMDBG environment
conda activate metamdbg1.4

# Compile the software
mkdir build
cd build
cmake ..
make -j 3

Building from source

git clone https://github.com/GaetanBenoitDev/metaMDBG.git
cd metaMDBG
mkdir build
cd build
cmake ..
make -j 3

Usage

Usage:  metaMDBG asm {OPTIONS}

 Basic options:
   --out-dir               Output dir for contigs and temporary files
   --in-hifi               PacBio HiFi read filename(s) (separated by space)
   --in-ont                Nanopore R10.4+ read filename(s) (separated by space)
   --threads               Number of cores [1]

# Nanopore assembly
metaMDBG asm --out-dir ./outputDir/ --in-ont reads.fastq.gz --threads 4
# Hifi assembly
metaMDBG asm --out-dir ./outputDir/ --in-hifi reads.fastq.gz --threads 4
# Multiple sample co-assembly
metaMDBG asm --out-dir ./outputDir/ --in-ont reads_A.fastq.gz reads_B.fastq.gz reads_C.fastq.gz --threads 4

MetaMDBG will generate polished contigs in outputDir ("contigs.fasta.gz").

Contig information

Contig information are contained in contig headers in the resulting fasta assembly file. Example:

>ctg112 length=7013 coverage=6 circular=yes
ACGTAGCTTATAGCGAGTATCG...
>ctg37 length=1988 coverage=3 circular=no
ATTATTGATTAGGGCTATGCAT...
>ctg82 length=3824 coverage=13 circular=no
AATTCCGGCGGCGTATTATTAC...

Headers are composed of several fields seperated by space.

• ctgID: the name of the contig
• length: the length of the contig in bps
• coverage: an estimated read coverage for the contig
• circular: whether the contig is circular or no

Resume an existing run (checkpoint system)

If an assembly run stops for any reason, simply resubmit the same command. MetaMDBG will automatically skip completed steps and resume from the last checkpoint.

Advanced usage

# Filter out reads with low average per-base quality (using phred score)
metaMDBG asm --out-dir ./outputDir/ --in-ont reads.fastq.gz --min-read-quality 10

# Filter output contigs (by length and by coverage)
metaMDBG asm --out-dir ./outputDir/ --in-ont reads.fastq.gz --min-contig-length 500 --min-contig-coverage 2

# Skip correction step (useful if using corrected reads)
metaMDBG asm --out-dir ./outputDir/ --in-ont reads.fastq.gz --skip-correction

# Filter out unique k-min-mers to improve performances.
# Useful for scaling to very large datasets, but may reduce assembly quality and completeness.
# By default, metaMDBG attempts to rescue low-abundance genomic k-min-mers.
metaMDBG asm --out-dir ./outputDir/ --in-ont reads.fastq.gz --min-abundance 2

# Stop assembly after reaching k-th iteration.
metaMDBG asm --out-dir ./outputDir/ --in-ont reads.fastq.gz --max-k 11

Generating an assembly graph

metaMDBG gfa --assembly-dir ./assemblyDir/ --k 21 --contigpath --readpath --threads 4

metaMDBG gfa --assembly-dir ./assemblyDir/ --k 0

metaMDBG gfa --assembly-dir ./assemblyDir/ --k 21

Results

Source data: mags.tsv errors.tsv perf.tsv

Alignment and binning were performed with minimap2 and SemiBin2. Completeness and contamination were measured with checkM2 (near-complete: ≥90% completeness and ≤5% contamination, Medium: ≥50% completeness and ≤5% contamination). Clipping events and zero-coverage regions were identified using the anvi-script-find-misassembly program from the Anvi’o platform. All assemblers were run with 32 cores.

Results on bacterial isolates

MetaMDBG was applied to bacterial isolate samples (each containing a single bacterial genome and, in some cases, multiple plasmids). The linked studies provide the original sequencing reads and the reference genomes assembled using Autocycler. Assembly quality was evaluated using QUAST.

License

metaMDBG is freely available under the MIT License.

Citation

• Gaetan Benoit, Sebastien Raguideau, Robert James, Adam M. Phillippy, Rayan Chikhi and Christopher Quince High-quality metagenome assembly from long accurate reads with metaMDBG, Nature Biotechnology (2023).

• Gaetan Benoit, Robert James, Sebastien Raguideau, Georgina Alabone, Tim Goodall, Rayan Chikhi and Christopher Quince High-quality metagenome assembly from nanopore reads with nanoMDBG, Nature Communications (2026).