Existing long-read assemblers require thousands of central processing unit hours to assemble a human genome and are being outpaced by sequencing technologies in terms of both throughput and cost. We developed a long-read assembler wtdbg2 (https://github.com/ruanjue/wtdbg2) that is 2–17 times as fast as published tools while achieving comparable contiguity and accuracy. It paves the way for population-scale long-read assembly in future.
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C. elegans and A. thaliana Ler-0 reads are available at the PacBio public datasets portal: http://bit.ly/pbpubdat. We downloaded SRR5439404 for the D. melanogaster A4 strain, SRR6702603 for the D. melanogaster reference ISO1 strain, ERR2571284 through ERR2571302 for M. schizocarpa (banana; MinION reads only), PRJNA378970 for axolotl, SRR7615963 for HG00733, and ERR2631600 and ERR2631601 for NA19240. CHM1 reads were acquired from SRP044331 (http://bit.ly/chm1p6c4 for raw signals), NA12878 reads from http://bit.ly/na12878ont (release 5) and NA24385 from http://bit.ly/NA24385ccs. For the A. thaliana Col-0/Cvi-0 dataset, the FASTQ files at SRA (AC, PRJNA314706) were not processed properly. J. Chin, the first author of the paper1 describing the dataset, provided us with reprocessed raw reads, which are now hosted at public file transfer protocol (FTP) site ftp://ftp.dfci.harvard.edu/pub/hli/col0-cvi0/. The CHM1 CANU and FALCON assemblies and the axolotl assembly are available at NCBI (GCA_000983455.1, GCA_001297185.1 and GCA_002915635.1, respectively). All the evaluated assemblies generated by us can be obtained at ftp://ftp.dfci.harvard.edu/pub/hli/wtdbg/. The FTP site also provides the detailed command lines and the FALCON configuration files.
The wtdbg2 source code is hosted by GitHub at: https://github.com/ruanjue/wtdbg2.
Chin, C. S. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods 13, 1050–1054 (2016).
Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).
Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017).
Li, H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32, 2103–2110 (2016).
Xiao, C. L. et al. MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Nat. Methods 14, 1072–1074 (2017).
De Coster, W. et al. Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome. Genome Res. 29, 1178–1187 (2019).
Myers, G. Efficient local alignment discovery amongst noisy long reads. in WABI vol. 8701. (eds. D. G. Brown & B. Morgenstern) 52–67, https://doi.org/10.1007/978-3-662-44753-6_5 (Springer, 2014).
Berlin, K. et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat. Biotechnol. 33, 623–630 (2015).
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
Chaisson, M. J., Wilson, R. K. & Eichler, E. E. Genetic variation and the de novo assembly of human genomes. Nat. Rev. Genet. 16, 627–640 (2015).
Smith, T. F. & Waterman, M. S. Identification of common molecular subsequences. J. Mol. Biol. 147, 195–197 (1981).
Ye, C., Ma, Z. S., Cannon, C. H., Pop, M. & Yu, D. W. Exploiting sparseness in de novo genome assembly. BMC Bioinforma. 13(Suppl 6), S1 (2012).
Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829 (2008).
Lee, C., Grasso, C. & Sharlow, M. F. Multiple sequence alignment using partial order graphs. Bioinformatics 18, 452–464 (2002).
Belser, C. et al. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nat. Plants 4, 879–887 (2018).
Chin, C. S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569 (2013).
Watson, M. & Warr, A. Errors in long-read assemblies can critically affect protein prediction. Nat. Biotechnol. 37, 124–126 (2019).
Jain, M. et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat. Biotechnol. 36, 338–345 (2018).
Nowoshilow, S. et al. The axolotl genome and the evolution of key tissue formation regulators. Nature 554, 50–55 (2018).
We are grateful to J. Chin for providing the properly processed raw reads for the A. thaliana Col-0/Cvi-0 dataset. We thank C. Ye from University of Maryland for frequent and fruitful discussion in the development of wtdbg and thank A. Li and S. Wu from CAAS for the help in polishing assemblies. We also thank the reviewers whose comments have helped us to improve wtdbg2. This study was supported by Natural Science Foundation of China (grant nos. 31571353 and 31822029 to J.R.) and by the US National Institutes for Health (grant no. R01-HG010040 to H.L.).
The authors declare no competing interests.
Peer review information Nicole Rusk and Lin Tang were the primary editors on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Evaluation of long-read assemblies: FALCON requires PacBio-style read names and does not work with ONT data or the A4 strain of D. melanogaster that was downloaded from SRA. The A. thaliana assembly by FALCON is acquired from PacBio website as our assembly is fragmented. MECAT produces fragmented assemblies for the ONT dataset. Human assemblies were performed by the developers of each assembler. Base-level evaluations and NGA50 are only reported when the sequenced strain or individual is close to the reference genome. BUSCO scores are computed for genomes sequenced to 50-fold coverage or higher.
The FALCON configure file for assembling C. elegans.
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Ruan, J., Li, H. Fast and accurate long-read assembly with wtdbg2. Nat Methods 17, 155–158 (2020). https://doi.org/10.1038/s41592-019-0669-3
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