Time- and memory-efficient genome assembly with Raven (original) (raw)

References

  1. 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).
    Article Google Scholar
  2. Chin, C.-S. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods 13, 1050–1054 (2016).
    Article Google Scholar
  3. Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).
    Article Google Scholar
  4. Li, H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32, 2103–2110 (2016).
    Article Google Scholar
  5. Shafin, K. et al. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nat. Biotechnol. 38, 1044–1053 (2020).
    Article Google Scholar
  6. Ruan, J. & Li, H. Fast and accurate long-read assembly with wtdbg2. Nat. Methods 17, 155–158 (2020).
    Article Google Scholar
  7. Kamath, G. M., Shomorony, I., Xia, F., Courtade, T. A. & Tse, D. N. HINGE: long-read assembly achieves optimal repeat resolution. Genome Res. 27, 747–756 (2017).
    Article Google Scholar
  8. Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017).
    Article Google Scholar
  9. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
    Article Google Scholar
  10. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
    Article Google Scholar
  11. Broder, A. Z. On the resemblance and containment of documents. In Proc. Compression and Complexity of SEQUENCES 1997 (cat. no. 97TB100171) (eds. Carpentieri, B. et al.) 21–29 (IEEE, 1997); https://doi.org/10.1109/SEQUEN.1997.666900
  12. Jain, C., Dilthey, A., Koren, S., Aluru, S. & Phillippy, A. M. A fast approximate algorithm for mapping long reads to large reference databases. In Research in Computational Molecular Biology (ed. Sahinalp, S. C.) 66–81 (Springer, 2017).
  13. Chin, C.-S. & Khalak, A. Human genome assembly in 100 minutes. Preprint at bioRxiv https://doi.org/10.1101/705616 (2019).
  14. Fruchterman, T. M. J. & Reingold, E. M. Graph drawing by force-directed placement. Softw. Pract. Exp. 21, 1129–1164 (1991).
    Article Google Scholar
  15. Barnes, J. & Hut, P. A hierarchical O(N_log_N) force-calculation algorithm. Nature 324, 446–449 (1986).
    Article Google Scholar
  16. Wick, R. R. & Holt, K. E. Benchmarking of long-read assemblers for prokaryote whole genome sequencing. F1000Res. 8, 2138 (2020).
    Article Google Scholar
  17. Nurk, S. et al. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Res. 30, 1291–1305 (2020).
    Article Google Scholar
  18. Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170–175 (2021).
    Article Google Scholar
  19. Belser, C. et al. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nat. Plants 4, 879–887 (2018).
    Article Google Scholar
  20. Choi, J. Y. et al. Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice. Genome Biol. 21, 21 (2020).
    Article Google Scholar
  21. Vaser, R. & Šikić, M. Yet another de novo genome assembler. In Proc. 2019 11th International Symposium on Image and Signal Processing and Analysis (ISPA) (eds. Lončarić, S. et al.) 147–151 (IEEE, 2019); https://doi.org/10.1109/ISPA.2019.8868909
  22. Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).
    Article Google Scholar
  23. Jain, M. et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat. Biotechnol. 36, 338–345 (2018).
    Article Google Scholar
  24. Mikheenko, A., Prjibelski, A., Saveliev, V., Antipov, D. & Gurevich, A. Versatile genome assembly evaluation with QUAST-LG. Bioinformatics 34, i142–i150 (2018).
    Article Google Scholar
  25. Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
    Article Google Scholar
  26. Vaser, R. & Sikic, M. 2021. Assemblies generated in the manuscript ‘Time and memory efficient genome assembly with Raven’. Zenodo https://doi.org/10.5281/zenodo.4443062
  27. Vaser, R. & Sikic, M. 2021. Raven source code used in the manuscript ‘Time and memory efficient genome assembly with Raven’. Zenodo https://doi.org/10.5281/zenodo.4672196

Download references