Omega: An Overlap-graph de novo Assembler for Metagenomics

Bioinformatics

Volumn 30, Issue 19, 2014, Pages 2717-2722

  Haider, Bahlul ^a   Ahn, Tae Hyuk ^a   Bushnell, Brian ^b   Chai, Juanjuan ^a   Copeland, Alex ^b   Pan, Chongle ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b U S DEPARTMENT OF ENERGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ALGORITHM; BACTERIAL GENOME; BIOLOGY; COMPUTER; COMPUTER LANGUAGE; COMPUTER PROGRAM; DNA SEQUENCE; INTERNET; METAGENOME; METAGENOMICS; PROCEDURES;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTERS; DNA, BACTERIAL; GENOME, BACTERIAL; INTERNET; METAGENOME; METAGENOMICS; PROGRAMMING LANGUAGES; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84911364768     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu395     Document Type: Article

References (19)

1. Butler, J. et al. (2008) ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res., 18, 810-820.
2. Goldberg, A.V. (1997) An efficient implementation of a scaling minimum-cost flow algorithm. J. Algorithms, 22, 1-29.
3. Haider, B. (2012) A New Algorithm for De Novo Genome Assembly. Department Computer Science, The University of Western Ontario.
4. Koren, S. et al. (2011) Bambus 2: scaffolding metagenomes. Bioinformatics, 27, 2964-2971.
5. Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
6. Li, H. and Durbin, R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595.
7. Li, R. et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res, 20, 265-272.
8. Myers, E.W. et al. (2000) A whole-genome assembly of Drosophila. Science, 287, 2196-2204.
9. Myers, E.W. (2005) The fragment assembly string graph. Bioinformatics, 21 (Suppl. 2), ii79-ii85.
10. Namiki, T. et al. (2012) MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res., 40, e155.
11. Peng, Y. et al. (2010) IDBA-A Practical Iterative de Bruijn Graph De Novo Assembler. In: Berger, B. (ed.) Research in Computational Molecular Biology. Berlin Heidelberg, Springer, pp. 426-440.
12. Peng, Y. et al. (2012) IDBA-UD: a de novo assembler for single-cell and meta-genomic sequencing data with highly uneven depth. Bioinformatics, 28, 1420-1428.
13. Pop, M. (2011) HMP Whole Metagenome Assembly.
14. Richter, D.C. et al. (2008) MetaSim: a sequencing simulator for genomics and meta-genomics. PloS One, 3, e3373.
15. Shakya, M. et al. (2013) Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ. Microbiol., 15, 1882-1899.
16. Simpson, J.T. and Durbin, R. (2012) Efficient de novo assembly of large genomes using compressed data structures. Genome Res., 22, 549-556.
17. Simpson, J.T. et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res., 19, 1117-1123.
18. Treangen, T.J. et al. (2013) MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol., 14, R2.
19. Zerbino, D.R. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829.