rust-mdbg: Minimizer-space de Bruijn graphs (mdBG) for whole-genome assembly

rust-mdbg is an ultra-fast minimizer-space de Bruijn graph (mdBG) implementation, geared towards the assembly of long and accurate reads such as PacBio HiFi.

Rationale

rust-mdbg performs mdBG construction of a 52x human genome HiFi data in around 10 minutes on 8 threads, with 10GB of maximum RAM usage.

rust-mdbg is fast because it operates in minimizer-space, meaning that the reads, the assembly graph, and the final assembly, are all represented as ordered lists of minimizers, instead of strings of nucleotides. A conversion step then yields a classical base-space representation.

Limitations

However, this high speed comes at a cost! :)

• rust-mdbg gives good-quality results but still of lower contiguity and completeness than state-of-the-art assemblers such as HiCanu and hifiasm.
• rust-mdbg performs best with at least 40x to 50x of coverage.
• No polishing step is implemented; so, assemblies will have around the same accuracy as the reads.
• Cannot assemble Nanopore data due to its higher error rate (see this comment)

Installation

Clone the repository (make sure you have a working Rust environment), and run

cargo build --release

Alternatively, you can install from bioconda:

conda install -c bioconda rust-mdbg

which has the Rust binaries, but not the additional scripts. For performing graph simplifications, gfatools is required.

Quick start

cargo build --release
target/release/rust-mdbg example/reads-0.00.fa.gz -k 7 --density 0.0008 -l 10 --minabund 2 --prefix example
utils/magic_simplify example

Multi-k assembly

For better contiguity, try the provided multi-k assembly script. It performs assembly iteratively, starting with k= 10, up to an automatically-determined largest k. This comes at the expense of ~7x longer running time.

utils/multik <reads.fq.gz> <some_output_prefix> <nb_threads>

Overview

rust-mdbg is a modular assembler. It consists of three components:

1. rust-mdbg, to perform assembly in minimizer-space
2. gfatools (external component), to perform graph simplifications
3. to_basespace, to convert a minimizer-space assembly to base-space

For convenience, components 2 and 3 are wrapped into a script called magic_simplify.

Input

rust-mdbg takes a single FASTA/FASTQ input (gzip-compressed or not). Multi-line sequences, and sequences with lowercase characters, are not supported.

If you have seqtk installed, you can use

seqtk seq -AU reads.unformatted.fq > reads.fa

to format reads accordingly.

Output data

The output of rust-mdbg consists of:

• A .gfa file containing the minimizer-space de Bruijn graph, without sequences,
• Several .sequences files containing the sequences of the nodes of the graph.

The executable to_basespace allows to combine both outputs and produce a .gfa file, with sequences.

Running an example

A sample set of reads is provided in the example/ folder. Run

target/release/rust-mdbg reads-0.00.fa.gz -k 7 --density 0.0008 -l 10 --minabund 2 --prefix example

which will create an example.gfa file.

In order to populate the .gfa file with base-space sequences and perform graph simplification, run

utils/magic_simplify example

which will create example.msimpl.gfa and example.msimpl.fa files.

Parameters

The main parameters of rust-mdbg are the k-min-mer value k, the minimizer length l, and the minimizer density d (delta in the paper). Another parameter is --presimp, set by default to 0.01, which performs a graph simplification: a neighbor node is deleted if its abundance is below 1% that of min(max(abundance of other neighbors), abundance of current node). For better results, and also without the need to set any parameter, try the multi-k strategy (see Multi-k assembly section). This section explains how parameters are set in single-k assembly.

All three parameters k, l, and d significantly impact the quality of results. One can think of them as a generalization of the k parameter in classical de Bruijn graphs. When you run rust-mdbg without specifying parameters, it sets them to:

d = 0.003

l = 12

k = 0.75 * average_readlen * d

These parameters will give reasonable, but far from optimal, draft assemblies. We experimentally found that the best results are often obtained with k values within 20-40, l within 10-14, and d within 0.001-0.005. Setting k and d such that the ratio k/d is slightly below the read length appears to be an effective strategy.

For further information on usage and parameters, run

target/release/rust-mdbg -h

for a one-line summary of each flag, or run

target/release/rust-mdbg --help

for a lengthy explanation of each flag.

Performance

Runtime breakdown:
H. sapiens: 10m23s = 6m51s rust-mdbg + 1m48s gfatools + 1m44s to_basespace

The runs with custom parameters (from the paper) were made with commit b99d938, and unlike in the paper, we did not use robust minimizers which requires additional l-mer counting beforehand. For historical reasons, reads and assemblies were homopolymer-compressed in those experiments and the homopolymer-compressed genome size is reported. So beware that these numbers are not directly comparable to the output of other assemblers. In addition to the parameters shown in the table, the rust-mdbg command line also contained --bf --no-error-correct --threads 8.

Running rust-mdbg without graph simplifications

To convert an assembly to base-space without performing any graph simplifications, there are two ways:

• with gfatools

gfatools asm -u  example.gfa > example.unitigs.gfa
target/release/to_basespace --gfa example.unitigs.gfa --sequences example

• without gfatools (slower, but the code is more straightforward to understand)

utils/complete_gfa.py example example.gfa

In both cases, this will create an example.complete.gfa file that you can convert to FASTA with

bash utils/gfa2fasta.sh example.complete

Metagenome assembly

Please refer to issue #30. In a nutshell, you may try parameters -k 21 -l 14 --density 0.003 as in the paper, and make sure to use the magic_simplify_meta script.

License

rust-mdbg is freely available under the MIT License.

Developers

• Barış Ekim, supervised by Bonnie Berger at the Computer Science and Artificial Intelligence Laboratory (CSAIL) at Massachusetts Institute of Technology (MIT)
• Rayan Chikhi at the Department of Computational Biology at Institut Pasteur

Citation

• Barış Ekim, Bonnie Berger, and Rayan Chikhi, Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer, Cell Systems (2021).
• Barış Ekim, Bonnie Berger, and Rayan Chikhi, Minimizer-space de Bruijn graphs, biorXiv preprint (2021).

@article {mdbg,
	author = {Ekim, Bar{\i}{\c s} and Berger, Bonnie and Chikhi, Rayan},
	title = {Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer},
	journal = {Cell Systems},
	year = {2021},
	issn = {2405-4712},
	doi = {https://doi.org/10.1016/j.cels.2021.08.009}
}

Contact

Should you have any inquiries, please contact Barış Ekim at baris [at] mit [dot] edu, or Rayan Chikhi at rchikhi [at] pasteur [dot] fr.