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Metagenome assembly of high-fidelity long reads with hifiasm-meta

Nature Methods volume 19, pages 671–674 (2022)Cite this article

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Abstract

De novo assembly of metagenome samples is a common approach to the study of microbial communities. Current metagenome assemblers developed for short sequence reads or noisy long reads were not optimized for accurate long reads. We thus developed hifiasm-meta, a metagenome assembler that exploits the high accuracy of recent data. Evaluated on seven empirical datasets, hifiasm-meta reconstructed tens to hundreds of complete circular bacterial genomes per dataset, consistently outperforming other metagenome assemblers.

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Fig. 1: Metagenome assemblies of empirical datasets.

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Data availability

HiFi data were obtained from NCBI Sequence Read Archive (SRA) with accession numbers shown in Table 1. All generated assemblies and underlying data for the figures are available at https://zenodo.org/record/6330282. ZymoBIOMICS mock reference genomes were downloaded from https://s3.amazonaws.com/zymo-files/BioPool/D6331.refseq.zip. The list of reference genomes in the ATCC mock community is available at https://www.atcc.org/products/msa-1003. CheckM database: https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz. GTDB-Tk database: https://data.ace.uq.edu.au/public/gtdb/data/releases/release95/95.0/auxillary_files/. Source data are provided with this paper.

Code availability

Hifiasm-meta is available at https://github.com/xfengnefx/hifiasm-meta.

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Acknowledgements

We thank W. Fan from Agricultural Genomics Institute, Shenzhen, China, for sharing the chicken gut dataset. This study was supported by US National Institutes of Health (grant R01HG010040 and U01HG010971, to H.L.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Author information

Authors and Affiliations

  1. Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA

    Xiaowen Feng, Haoyu Cheng & Heng Li

  2. Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA

    Xiaowen Feng, Haoyu Cheng & Heng Li

  3. Pacific Biosciences, Menlo Park, CA, USA

    Daniel Portik

Authors
  1. Xiaowen Feng
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  2. Haoyu Cheng
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  4. Heng Li
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Contributions

X.F. and H.L. conceived the project, designed the algorithm and wrote the manuscript. X.F. implemented the algorithm and evaluated the metagenome assemblies. H.C. helped with the algorithm implementation. D.P. helped with assembly evaluations. All authors helped with the data analysis and revised the manuscript.

Corresponding author

Correspondence to Heng Li.

Ethics declarations

Competing interests

D.P. is an employee of Pacific Biosciences. H.L. is a consultant of Integrated DNA Technologies and on the Scientific Advisory Boards of Sentieon and Innozeen. The remaining authors declare no competing interests.

Peer review

Peer review information

Nature Methods thanks Mads Albertsen and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Lei Tang was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 The hifiasm-meta assembly graph of the sheepA dataset.

Short disconnected contigs are not shown.

Source data

Extended Data Fig. 2 Yak QV score correlated with contig coverage.

Plots showing >1Mb contigs in sheepB assemblies. Contig coverage was estimated by jgi_summarize_bam_contig_depths from metabat2, and alignment was done with minimap2 -a -k 19 -w 10 -I 10G -g 5000 -r 2000 –lj-min-ratio 0.5 -A 2 -B 5 -O 5,56 -E 4,1 -z 400,50. Hifiasm-meta assembled 37 contigs without k-mer errors. HiCanu and metaFlye each assembled 4 contigs without k-mer errors.

Source data

Supplementary information

Reporting Summary

Supplementary Tables

Supplementary Tables 1–6.

Source data

Source Data Fig. 1

The data points used to plot Fig. 1.

Source Data Extended Data Fig. 1

Instruction for redirecting the interested reader to data release (on Zenodo) for the assembly graph, which is the underlying data for Extended Data Fig. 1.

Source Data Extended Data Fig. 2

The data points used to plot Extended Data Fig. 2.

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Feng, X., Cheng, H., Portik, D. et al. Metagenome assembly of high-fidelity long reads with hifiasm-meta. Nat Methods 19, 671–674 (2022). https://doi.org/10.1038/s41592-022-01478-3

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