hAssembler: A hybrid de novo genome assembly approach for large genomes

AMIT KAIRI; PRIYANKA GUHA MAJUMDAR; ATMAKURI RAMAKRISHNA RAO

doi:10.56093/ijas.v90i10.107981

Authors

AMIT KAIRI Research Scholar, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110 012, India
PRIYANKA GUHA MAJUMDAR Research Scholar, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110 012, India
ATMAKURI RAMAKRISHNA RAO Principal Scientist, Centre for Agricultural Bioinformatics (CABin), ICAR-IASRI, Pusa, New Delhi

https://doi.org/10.56093/ijas.v90i10.107981

Keywords:

DBG, Hybrid genome assembly, Illumina, OLC, Long Reads, PacBio, Short reads

Abstract

Genome assembly is a process where large contigs and scaffolds are constructed from raw reads generated by sequencing machines. Based on the size of the generated reads they can be primarily categorized into short reads and long reads. Modern genome assemblers follow De Bruijn Graph (DBG) approach for assembly of short reads, whereas Overlap Layout Consensus (OLC) approach for assembly of long reads. For de novo genome assembly, DBG based assemblers are very efficient at repeat resolution but are computation intensive and sensitive to sequencing errors. On the other hand, OLC based assemblers are intuitive and very time efficient but not efficient at resolving repeat regions. Here, we developed an hAssembler, which leverages the advantages of both DBG and OLC approaches and compared its performance with the existing hybrid assemblers. It uses both long reads and short reads and run OLC and DBG in parallel. By using both the long and short reads, the time complexity of hAssembler was reduced considerably. The results showed that hAssembler outperformed the existing hybrid assemblers in terms of time and performance (N50) while assembling the large genomes.

Downloads

Download data is not yet available.

References

Au K F, Underwood J G, Lee L and Wong W H. 2012. Improving PacBio long read accuracy by short read alignment. PloS One 7(10): e46679. DOI: https://doi.org/10.1371/journal.pone.0046679

Batzoglou S, Jaffe D B, Stanley K, Butler J, Gnerre S, Mauceli E and Lander E S. 2002. ARACHNE: a whole-genome shotgun assembler. Genome Research 12(1): 177-189.

Butler J, MacCallum I, Kleber M, Shlyakhter I A, Belmonte M K, Lander E S and Jaffe D B. 2008. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Research 18(5):810-820. DOI: https://doi.org/10.1101/gr.7337908

Compeau P E, Pevzner P A and Tesler G. 2011. How to apply de Bruijn graphs to genome assembly. Nature Biotechnology 29(11): 987. DOI: https://doi.org/10.1038/nbt.2023

Denisov G, Walenz B, Halpern A L, Miller J, Axelrod N, Levy S and Sutton G. 2008. Consensus generation and variant detection by Celera Assembler. Bioinformatics 24(8): 1035-1040. DOI: https://doi.org/10.1093/bioinformatics/btn074

Deshpande V, Fung E D, Pham S and Bafna V. 2013. Cerulean: A hybrid assembly using high throughput short and long reads. (In) International workshop on algorithms in bioinformatics, Springer, Berlin, Heidelberg, pp 349-363. DOI: https://doi.org/10.1007/978-3-642-40453-5_27

Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J and Paten B. 2011. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research 21(12): 2224–2241. doi:10.1101/gr.126599.111 DOI: https://doi.org/10.1101/gr.126599.111

Gordon D, Huddleston J, Chaisson M J, Hill C M, Kronenberg Z N, Munson K M and Dunn C. 2016. Long-read sequence assembly of the gorilla genome. Science 352(6281): aae0344. DOI: https://doi.org/10.1126/science.aae0344

Green P. 1994. Phrap. (http://www.genome.washington.edu/ UWGC/analysistools/phrap.htm).

Huang X and Madan A. 1999. CAP3: A DNA sequence assembly program. Genome Rresearch 9(9): 868-877. DOI: https://doi.org/10.1101/gr.9.9.868

Kiełbasa S M, Wan R, Sato K, Horton P and Frith M C. 2011. Adaptive seeds tame genomic sequence comparison. Genome Research 21(3): 487-493. DOI: https://doi.org/10.1101/gr.113985.110

Koren S, Schatz M C, Walenz B P, Martin J, Howard J T, Ganapathy G and Phillippy A M. 2012. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology 30(7): 693. DOI: https://doi.org/10.1038/nbt.2280

Lander E S, Linton L M, Birren B, Nusbaum C, Zody M C, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R et al. 2001. Initial sequencing and analysis of the human genome. Nature 409 (6822): 860-921. DOI: https://doi.org/10.1038/35057062

Lapidus A, Antipov D, Bankevich A, Gurevich A, Korobeynikov A, Nurk S, Prjibelski A, Safonova Y, Vasilinetc I, Pevzner P A. 2013. New Frontiers of Genome Assembly with SPAdes 3.0. (poster).

Laver T, Harrison J, O’neill P A, Moore K, Farbos A, Paszkiewicz K, and Studholme D J. 2015. Assessing the performance of the Oxford nanopore technologies MinION. Biomolecular Detection and Quantification 3: 1-8. DOI: https://doi.org/10.1016/j.bdq.2015.02.001

Lee H, Gurtowski J, Yoo S, Marcus S, McCombie W R and Schatz M. 2014. Error correction and assembly complexity of single molecule sequencing reads. BioRxiv: 006395. DOI: https://doi.org/10.1101/006395

Miclotte G, Heydari M, Demeester P, Rombauts S, Van de Peer Y, Audenaert P and Fostier J. 2016. Jabba: hybrid error correction for long sequencing reads. Algorithms for Molecular Biology 11(1):10. DOI: https://doi.org/10.1186/s13015-016-0075-7

Mullikin J C and Ning Z. 2003. The phusion assembler. Genome Rresearch 13(1): 81-90. DOI: https://doi.org/10.1101/gr.731003

Paul H, Chen R, Durbin K J, Egan A, Ren Y, Song X, Weinstock G M and Gibbs R A. 2004. The Atlas genome assembly system. Genome Research 14(4): 721-732. DOI: https://doi.org/10.1101/gr.2264004

Pop M, Phillippy A, Delcher A L and Salzberg S L. 2004. Comparative genome assembly. Briefings in Bioinformatics 5(3): 237-248. DOI: https://doi.org/10.1093/bib/5.3.237

Salmela L and Rivals E. 2014. LoRDEC: accurate and efficient long read error correction. Bioinformatics, 30(24): 3506-3514. DOI: https://doi.org/10.1093/bioinformatics/btu538

Wang J, Wong G K S, Ni P, Han Y, Huang X, Zhang J and Xu X. 2002. RePS: a sequence assembler that masks exact repeats identified from the shotgun data. Genome Research 12(5): 824-831. DOI: https://doi.org/10.1101/gr.165102

Ye C, Hill C M, Wu S, Ruan J, and Ma Z S. 2016. DBG2OLC: efficient assembly of large genomes using long erroneous reads of the third-generation sequencing technologies. Scientific Reports 6 : 31900. DOI: https://doi.org/10.1038/srep31900

Zerbino D and Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18(5):821-829. DOI: https://doi.org/10.1101/gr.074492.107