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Time- and memory-efficient genome assembly with Raven

Nature Computational Science volume 1, pages 332–336 (2021)Cite this article

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A preprint version of the article is available at bioRxiv.

Abstract

Whole genome sequencing technologies are unable to invariably read DNA molecules intact, a shortcoming that assemblers try to resolve by stitching the obtained fragments back together. Here, we present methods for the improvement of de novo genome assembly from erroneous long reads incorporated into a tool called Raven. Raven maintains similar performance for various genomes and has accuracy on par with other assemblers that support third-generation sequencing data. It is one of the fastest options while having the lowest memory consumption on the majority of benchmarked datasets.

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Fig. 1: Bacterial assembly graph drawn with the force-directed placement algorithm.

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Data availability

The ONT dataset for A. thaliana is available under accession no. ERR2173373, for D. melanogaster under SRR6702603, for H. sapiens NA12878 at https://github.com/nanopore-wgs-consortium/NA12878 (release 6), for H. sapiens CHM13 at https://github.com/marbl/CHM13 (release 6), for H. sapiens HG002 at https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/Ultralong_OxfordNanopore/guppy-V3.4.5/ and for H. sapiens HG00733 at https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=NHGRI_UCSC_panel/HG00733/nanopore/. The PacBio CLR dataset for A. thaliana is available at https://downloads.pacbcloud.com/public/SequelData/ArabidopsisDemoData/, for D. melanogaster under accession no. SRR5439404, for H. sapiens CHM13 at https://github.com/marbl/CHM13 (extracted from draft v1.0 bam), for H. sapiens HG002 at https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/PacBio_MtSinai_NIST/PacBio_fasta/ and for H. sapiens HG0073 under SRR7615963. The PacBio HiFi dataset for H. sapiens CHM13 is available from accession nos. SRR11292120–SRR11292123, for H. sapiens HG002 under SRR10382244, SRR10382245, SRR10382248 and SRR10382249, and for H. sapiens HG00733 under ERX3831682. Illumina reads for yak evaluation are available from accession nos. SRX1049768–SRX1049782 for H. sapiens NA12878, from https://github.com/marbl/CHM13 (extracted from draft v1.0 bam) for H. sapiens CHM13, from https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/NIST_HiSeq_HG002_Homogeneity-10953946/NHGRI_Illumina300X_AJtrio_novoalign_bams/ (extracted from 60x bam) for H. sapiens HG002 and under accession no. SRR7782677 for H. sapiens HG00733. ONT plant datasets are available under accession nos. ERR2564160–ERR2564170 for B. rapa, from ERR2564373–ERR2564382 for B. oleracea, from ERR2571286–ERR2571303 for M. schizocarpa, from ERR3476478–ERR3476482 for O. sativa basmati 334 and from ERR3476463–ERR3476466 for O. sativa dom sufid. All generated assemblies in this research are available at Zenodo26.

Code availability

The Raven source code is available under an MIT license on GitHub at https://github.com/lbcb-sci/raven. Source code for version 1.3.0 used in this manuscript is also available at Zenodo27.

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Acknowledgements

This work has been supported in part by the Croatian Science Foundation under the project ‘Single genome and metagenome assembly’ (IP-2018-01-5886, to M.Š.), the European Regional Development Fund under grant no. KK.01.1.1.01.0009 (DATACROSS, to M.Š.) and the A*STAR Computational Resource Centre through the use of their high-performance computing facilities. R.V. and M.Š. have been partially supported by funding from A*STAR, Singapore. We acknowledge Intel Corporation for allowing us to test with the Intel Optane persistent memory server and providing us with high-quality technical support. Finally, we thank G. Žužić from Carnegie Mellon University for valuable discussions about graph drawings.

Author information

Authors and Affiliations

  1. Laboratory for Bioinformatics and Computational Biology, Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia

    Robert Vaser & Mile Šikić

  2. Laboratory of AI in Genomics, Genome Institute of Singapore, A*STAR, Singapore, Singapore

    Robert Vaser & Mile Šikić

Authors
  1. Robert Vaser
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  2. Mile Šikić
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Contributions

M.Š. devised the project. R.V. designed and implemented Raven, and benchmarked it with other assemblers. Both authors drafted and revised the manuscript.

Corresponding author

Correspondence to Mile Šikić.

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The authors declare no competing interests.

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Peer review information Nature Computational Science thanks the anonymous reviewers for their contribution to the peer review of this work. Handling editor: Ananya Rastogi, in collaboration with the Nature Computational Science team.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–4 and Tables 1–5.

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Vaser, R., Šikić, M. Time- and memory-efficient genome assembly with Raven. Nat Comput Sci 1, 332–336 (2021). https://doi.org/10.1038/s43588-021-00073-4

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