mapquik: Efficient low-divergence mapping of long reads in minimizer space

mapquik is an ultra-fast read mapper based on $k$-min-mers (matches of $k$ consecutively-sampled minimizers). It aligns long and accurate reads such as PacBio HiFi to a reference genome.

Rationale

Limitations

Installation

Pre-requisites: a working Rust environment (https://rustup.rs/).

Clone the repository, and run

rustup install nightly
cargo +nightly build --release

The nightly version of cargo is required because mapquik uses experimental language features (such as SIMD and intrinsics).

Quick start

target/release/mapquik <reads.fq> --reference <reference.fa>

Input

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

Output

The output of mapquik is a regular PAF file.

Running an example

An example reference genome, and a script to simulate reads using pbsim are provided in the example/ folder. To run mapquik on a small set of 100 reads, type:

cd example && bash run_ecoli.sh

which will run both mapquik and minimap2 on 100 simulated reads, and return the output of paftools.js mapeval on both PAF files.

To simulate a larger set of reads using pbsim and map, type:

bash simulate_pbsim.sh && bash run_ecoli_full.sh

Parameters

For further information on usage and parameters, run

target/release/mapquik -h

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

target/release/mapquik --help

for a lengthy explanation of each flag.

Data Availability

All scripts used to generate the figures and tables in the paper can be found in the experiments/ folder. Specifically, the simulate_chm13.sh and simulate_maize.sh scripts can be used similarly to simulate reads.

In order to obtain and map DeepConsensus reads, first run

wget https://storage.googleapis.com/brain-genomics-public/research/deepconsensus/data/v0.3/assembly_analysis/fastqs/HG002_24kb_2SMRT_cells.dc.v0.3.q20.fastq.gz
gunzip -c HG002_24kb_2SMRT_cells.dc.v0.3.q20.fastq.gz | grep -v TOTAL > dc.hg002.fastq

and map to a reference genome reference.fa in your directory with mapquik using

target/release/mapquik dc.hg002.fastq --reference reference.fa -p mapquik-dc

Performance

License

mapquik 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

mapquik is not yet published. For now, please cite our original mdBG article: Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer (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},
	year = {2021},
	doi = {10.1016/j.cels.2021.08.009},
	journal = {Cell Systems}
	volume={12},
  	number={10},
  	pages={958--968},
  	year={2021},
  	publisher={Elsevier}
}

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.