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-mdbggives good-quality results but still of lower contiguity and completeness than state-of-the-art assemblers such as HiCanu and hifiasm.rust-mdbgperforms 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.
Installation
Clone the repository (make sure you have a working Rust environment), and run
cargo build --release
For performing graph simplifications, gfatools is required.
Quick start
cargo build --release
target/release/rust-mdbg 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:
rust-mdbg, to perform assembly in minimizer-spacegfatools(external component), to perform graph simplificationsto_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 -A reads.unformatted.fq > reads.fa
to format reads accordingly.
Output data
The output of rust-mdbg consists of:
- A
.gfafile containing the minimizer-space de Bruijn graph, without sequences, - Several
.sequencesfiles 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
| Dataset | Genome size (HPC) | Coverage |
Parameters
|
N50 | Runtime | Memory |
|---|---|---|---|---|---|---|
| D. melanogaster HiFi | 98Mbp | 100x | auto multi- kk=35,l=12,d=0.002 |
2.5Mbp 2.5Mbp 6.0Mbp |
2m15s 15m 1m9s |
2.5GB 1.8GB 1.5GB |
| Strawberry HiFi | 0.7Gbp | 36x | auto multi- kk=38,l=14,d=0.003 |
0.5Mbp 1Mbp 0.7Mbp |
6m12s 40m 5m31s |
12GB 11GB 10GB |
| H. sapiens (HG002) HiFi | 2.2Gbp | 52x | auto multi- kk=21,l=14,d=0.003 |
1.0Mbp 16.9Mbp 13.9Mbp |
27m30s 3h15m 10m23s |
16.9GB 20GB 10.1GB |
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.sequences
- without
gfatools(slower, but the code is more straightforward to understand)
utils/complete_gfa.py example.sequences 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
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
Minimizer-space de Bruijn graphs (2021) BiorXiv
@article {mdbg,
author = {Ekim, Bar{\i}{\c s} and Berger, Bonnie and Chikhi, Rayan},
title = {Minimizer-space de Bruijn graphs},
year = {2021},
doi = {10.1101/2021.06.09.447586},
publisher = {Cold Spring Harbor Laboratory},
journal = {bioRxiv}
}
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.
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