Assembling short reads from jumping libraries with large insert sizes

Bioinformatics

Volumn 31, Issue 20, 2015, Pages 3262-3268

  Vasilinetc, Irina ^a   Prjibelski, Andrey D ^a,b   Gurevich, Alexey ^a,b   Korobeynikov, Anton ^a,b   Pevzner, Pavel A ^b,c  

^a ST PETERSBURG ACADEMIC UNIVERSITY   (Russian Federation)

^b ST PETERSBURG STATE UNIVERSITY   (Russian Federation)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BACTERIAL GENOME; DNA SEQUENCE; GENE LIBRARY; GENOMICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES;

ALGORITHMS; GENE LIBRARY; GENOME, BACTERIAL; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ANALYSIS, DNA;

EID: 84947745303     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv337     Document Type: Article

References (23)

1. Bankevich, A. et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol., 19, 455-477.
2. Blattner, F.R. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453-1462.
3. Boetzer, M. et al. (2011) Scaffolding pre-assembled contigs using SSPACE. Bioinformatics, 27, 578-579.
4. Boisvert, S. et al. (2010) Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J. Comput. Biol., 17, 1519-1533.
5. Bresler, M. et al. (2012) Telescoper: de novo assembly of highly repetitive regions. Bioinformatics, 28, 311-317.
6. Chaisson, M. et al. (2009) De novo fragment assembly with short mate-paired reads: does the read length matter. Genome Res., 19, 336.
7. Chin, C.-S. et al. (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods, 10, 563-569.
8. Chitsaz, H. et al. (2011) Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat. Biotechnol., 29, 915-921.
9. Dayarian, A. et al. (2010) SOPRA: Scaffolding algorithm for paired reads via statistical optimization. BMC Bioinformatics, 11, 345.
10. Donmez, N., Brudno, M. (2013) SCARPA: scaffolding reads with practical algorithms. Bioinformatics, 29, 428-434.
11. Gao, S. et al. (2011) Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. J. Comput. Biol., 18, 1681-1691.
12. Gnerre, S. et al. (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl. Acad. Sci. USA., 108, 1513.
13. Gurevich, A. et al. (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics, 29, 1072-1075.
14. Li, R. et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res., 20, 265-272.
15. Peng, Y. et al. (2012) IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics, 28, 1-8.
16. Pevzner, P.A. et al. (2001) An Eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci. USA., 98, 9748-9753.
17. Pop, M. et al. (2004) Hierarchical scaffolding with Bambus. Genome Res., 14, 149-159.
18. Prjibelski, A.D. et al. (2014) ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics, 30, i293-i301.
19. Simpson, J. et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res., 19, 1117-1123.
20. Tindall, B.J. et al. (2010) Complete genome sequence of Meiothermus ruber type strain (21T). Stand. Genomic Sci., 3, 26-36.
21. Vyahhi, N. et al. (2012) From de Bruijn graphs to rectangle graphs for genome assembly. In: Raphael, B., Tang, J. (eds) Workshop on Algorithms in Bioinformatics 2012, volume 7534 of Lecture Notes in Computer Science, Springer Berlin Heidelberg, pp. 200-212.
22. Zerbino, D.R., Birney, E. (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829.
23. Zhu, X. et al. (2014) PERGA: a paired-end read guided de novo assembler for extending contigs using SVM and look ahead approach. PLoS One, 9, e114253.