Genome assembly from synthetic long read clouds

Bioinformatics

Volumn 32, Issue 12, 2016, Pages i216-i224

  Kuleshov, Volodymyr ^a,b   Snyder, Michael P ^b   Batzoglou, Serafim ^a  

^a Stanford University   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCE; GENOME; GENOMICS; HIGH THROUGHPUT SEQUENCING;

GENOME; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ANALYSIS, DNA;

EID: 84976499731     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw267     Document Type: Article

References (31)

1. Adey,A. et al. (2014) In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res., 24, 2041-2049.
2. Amini,S. et al. (2014) Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat. Genet., 46, 1343-1349.
3. Bankevich,A. et al. (2012) Spades: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol., 19, 455-477.
4. Berlin,K. et al. (2015) Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat. Biotechnol., 33, 623-630.
5. Bishara,A. et al. (2015) Read clouds uncover variation in complex regions of the human genome. Genome Res., 25, 1570-1580.
6. Boetzer,M. et al. (2011) Scaffolding pre-assembled contigs using S SPACE. Bioinformatics, 27, 578-579.
7. Burton,J.N. et al. (2013) Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol., 31, 1119-1125.
8. Burton,J.N. et al (2014) Species-level deconvolution of metagenome assemblies with hi-c-based contact probability maps. G3, 4, 1339-1346.
9. Chaisson,M. et al. (2009) De novo fragment assembly with short mate-paired reads: Does the read length matter Genome Res., 19, 336.
10. Chaisson,M.J.P. et al. (2015) Resolving the complexity of the human genome using single-molecule sequencing. Nature, 517, 608-611.
11. Chin,C.S. et al. (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods, 10, 563-569.
12. Duitama,J. et al. (2012) Fosmid-based whole genome haplotyping of a HapMap trio child: Evaluation of single individual haplotyping techniques. Nucleic Acids Res., 40, 2041-2053.
13. Gurevich,A. et al. (2013) QUAST: Quality assessment tool for genome assemblies. Bioinformatics, 29, 1072-1075.
14. Human Microbiome Project Consortium. (2012) A framework for human microbiome research. Nature, 486, 215-221.
15. Hunt,M. et al. (2014) A comprehensive evaluation of assembly scaffolding tools. Genome Biol., 15, 1-15.
16. Koren,S. et al. (2012) Hybrid error correction and de novo assembly of singlemolecule sequencing reads. Nat. Biotechnol., 30, 693-700.
17. Kuleshov,V. (2014) Probabilistic single-individual haplotyping. Bioinformatics, 30, 379-385.
18. Kuleshov,V. et al. (2014) Whole-genome haplotyping using long reads and statistical methods. Nat. Biotechnol., 32, 261-266.
19. Kuleshov,V. et al. (2015) Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nat. Biotech., 34, 64-69.
20. Li,R. et al. (2015) Illumina synthetic long read sequencing allows recovery of missing sequences even in the finished C. elegans genome. Sci. Rep., 5, 10814.
21. Luo,R. et al. (2012) Soapdenovo2: An empirically improved memory-efficient short-read de novo assembler. GigaScience, 1, 1.
22. McCoy,R.C. et al. (2014) Illumina truseq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements. PLoS One, 9, e106689.
23. Myers,E.W. et al. (2000) A whole-genome assembly of drosophila. Science, 287, 2196-2204.
24. Peters,B.A. et al. (2012) Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature, 487, 190-195.
25. Pevzner,P.A. et al. (2001) An Eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci. USA, 98, 9748-9753.
26. Salzberg,S.L. et al. (2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res., 22, 557-567.
27. Sharon,I. et al. (2015) Accurate, multi-kb reads resolve complex populations and detect rare microorganisms. Genome Res., 25, 534-543.
28. Simpson,J.T. and Durbin,R. (2011) Efficient de novo assembly of large genomes using compressed data structures.Genome Res., 22, 126953.111-126556.gr.
29. Sommer,D.D. et al. (2007) Minimus: A fast, lightweight genome assembler. BMC Bioinformatics, 8, 64.
30. Voskoboynik,A. et al. (2013) The genome sequence of the colonial chordate, Botryllus schlosseri. eLife, 2, e00569.
31. Zerbino,D.R. et al. (2009) Pebble and rock band: Heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PLoS One, 4, e8407.