HINGE: Long-read assembly achieves optimal repeat resolution

Genome Research

Volumn 27, Issue 5, 2017, Pages 747-756

  Kamath, Govinda M ^a   Shomorony, Ilan ^b   Xia, Fei ^a   Courtade, Thomas A ^b   Tse, David N ^a,b  

^a Stanford University   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; GENETIC ALGORITHM; GENETIC DATABASE; GENOMICS; NONHUMAN; PRIORITY JOURNAL; ANIMAL; COMPARATIVE STUDY; CONTIG MAPPING; DNA SEQUENCE; HUMAN; NUCLEOTIDE REPEAT; PROCEDURES; SOFTWARE; STANDARDS;

ANIMALS; CONTIG MAPPING; GENOMICS; HUMANS; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 85019103020     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.216465.116     Document Type: Article

References (29)

1. Bastian M, Heymann S, Jacomy M. 2009. Gephi: an open source software for exploring and manipulating networks. ICWSM 8: 361-362.
2. Berlin K, Koren S, Chin C-S, Drake JP, Landolin JM, Phillippy AM. 2015. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol 33: 623-630.
3. Bresler G, Bresler M, Tse D. 2013. Optimal assembly for high throughput shotgun sequencing. BMC Bioinformatics 14: S18.
4. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. 2008. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 18: 810-820.
5. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10: 563-569.
6. Chin C-S, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, et al. 2016. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods 13: 1050-1054.
7. Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA, Harris SR. 2015. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol 16: 294.
8. Koren S, Harhay GP, Smith TPL, Bono JL, Harhay DM, Mcvey SD, Radune D, Bergman NH, Phillippy AM. 2013. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biol 14: R101.
9. Li H. 2016. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32: 2103-2110.
10. Lien S, Koop BF, Sandve SR, Miller JR, KentMP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A. 2016. The Atlantic salmon genome provides insights into rediploidization. Nature 533: 200-205.
11. Lin Y, Yuan J, Kolmogorov M, Shen MW, Chaisson M, Pevzner PA. 2016. Assembly of long error-prone reads using de Bruijn graphs. Proc Natl Acad Sci 113: E8396-E8405.
12. Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G. 2008. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24: 2818-2824.
13. Mulyukov Z, Pevzner PA. 2002. EULER-PCR: finishing experiments for repeat resolution. Pac Symp Biocomput 199-210.
14. Myers EW. 1995. Toward simplifying and accurately formulating fragment assembly. J Comput Biol 2: 275-290.
15. Myers EW. 2005. The fragment assembly string graph. Bioinformatics 21: i79-ii85.
16. Myers EW. 2014. Efficient local alignment discovery amongst noisy long reads. Lect Notes Comput Sci 52-67.
17. Myers EW. 2016a. A history of DNA sequence assembly. Inf Technol 58: 126-132.
18. Myers EW. 2016b. https://github.com/thegenemyers/DAZZ-DB.
19. MyersEW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KH, Remington KA, et al. 2000. A whole-genome assembly of Drosophila. Science 287: 2196-2204.
20. Nagarajan N, Pop M. 2009. Parametric complexity of sequence assembly: theory and applications to next generation sequencing. J Comput Biol 16: 897-908.
21. Peng Y, Yu P, Leung HCM, Yiu SM, Chin FYL. 2010. IDBA-a practical iterative de Bruijn graph de novo assembler. Lect Notes Comput Sci 426-440.
22. Pevzner PA. 1995. DNA physical mapping and alternating Eulerian cycles in colored graphs. Algorithmica 13: 77-105.
23. Pevzner PA, Tang H. 2001. Fragment assembly with double-barreled data. Bioinformatics 17(Suppl 1): S225-S233.
24. Shomorony I, Kamath GM, Xia F, Courtade TA, Tse DNC. 2016a. Partial DNA assembly: a rate-distortion perspective. IEEE International Symposium on Information Theory 2016, pp. 1799-1803.
25. Shomorony I, Kim SH, Courtade TA, Tse DNC. 2016b. Information-optimal genome assembly via sparse read-overlap graphs. Bioinformatics 32: i494-i502.
26. Tarhio J, Ukkonen E. 1988. A greedy approximation algorithm for constructing shortest common superstrings. Theor Comput Sci 57: 131-145.
27. Tørresen OK, Star B, Jentoft S, Reinar WB, Grove H, Miller JR, Walenz BP, Knight J, Ekholm JM, Peluso P. 2017. An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics 18: 95.
28. Ukkonen E. 1992. Approximate string-matching with q-grams and maximal matches. Theor Comput Sci 92: 191-211.
29. Vaser R, Sović I, Nagarajan N, Šikić M. 2017. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res (this issue). doi: 10.1101/gr.214270.116.