Reference-independent comparative metagenomics using cross-assembly: CrAss

Bioinformatics

Volumn 28, Issue 24, 2012, Pages 3225-3231

  Dutilh, Bas E ^a,b,c   Schmieder, Robert ^b,d   Nulton, Jim ^c   Felts, Ben ^c   Salamon, Peter ^c   Edwards, Robert A ^b,e   Mokili, John L ^c  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^b San Diego State University   (United States)

^c SAN DIEGO STATE UNIVERSITY   (United States)

^d SAN DIEGO STATE UNIVERSITY   (United States)

^e ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER PROGRAM; HUMAN; METAGENOME; METAGENOMICS; METHODOLOGY; VIRUS GENOME;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENOME, VIRAL; HUMANS; METAGENOME; METAGENOMICS; SOFTWARE;

EID: 84870829895     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts613     Document Type: Article

References (35)

1. Amari, S.-I. (1982) Differential geometry of curved exponential families-curvatures and information loss. Ann. Stat., 10, 357-385.
2. Angly, F. et al. (2005) PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics, 6, 41.
3. Angly, F.E. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol., 4, e368.
4. Angly, F.E. et al. (2012) Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic Acids Res., 40, e94.
5. Balzer, S. et al. (2011) Systematic exploration of error sources in pyrosequencing flowgram data. Bioinformatics, 27, i304-i309.
6. Bonhoeffer, S. and Sniegowski, P. (2002) Virus evolution: the importance of being erroneous. Nature, 420, 367-369.
7. Camacho, C. et al. (2009) BLAST\+: architecture and applications. BMC Bioinformatics, 10, 421.
8. Chevreux, B. et al. (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res., 14, 1147-1159.
9. Dutilh, B.E. et al. (2004) The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J. Mol. Evol., 58, 527-539.
10. Dutilh, B.E. et al. (2011) FACIL: Fast and Accurate Genetic Code Inference and Logo. Bioinformatics, 27, 1929-1933.
11. Dutilh, B.E. et al. (2007) Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinformatics, 23, 815-824.
12. Felsenstein, J. (1989) PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164-166.
13. Gascuel, O. (1997) BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol., 14, 685-695.
14. Ghosh, T.S. et al. (2011) HabiSign: a novel approach for comparison of metagenomes and rapid identification of habitat-specific sequences. BMC Bioinformatics, 12 (Suppl. 13), S9.
15. Hofacker, I.L. and Stadler, P.F. (2006) Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics, 22, 1172-1176.
16. Karlin, S. and Mrazek, J. (1997) Compositional differences within and between eukaryotic genomes. Proc. Natl Acad. Sci. USA, 94, 10227-10232.
17. Korbel, J.O. et al. (2002) SHOT: a web server for the construction of genome phylogenies. Trends Genet., 18, 158-162.
18. Li, J.W. et al. (2012) SEQanswers: an open access community for collaboratively decoding genomes. Bioinformatics, 28, 1272-1273.
19. Li, Z. et al. (2011) Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph. Brief. Funct. Genomics, 11, 25-37.
20. Lin, Y. et al. (2011) Comparative studies of de novo assembly tools for next-generation sequencing technologies. Bioinformatics, 27, 2031-2037.
21. Lopez-Bueno, A. et al. (2009) High diversity of the viral community from an Antarctic lake. Science, 326, 858-861.
22. Margulies, M. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
23. Meyer, F. et al. (2008) The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics, 9, 386.
24. Mokili, J.L. et al. (2012) Metagenomics and future perspectives in virus discovery. Curr. Opin. Virol., 2, 1-15.
25. Nakamura, S. et al. (2009) Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One, 4, e4219.
26. Pruitt, K.D. et al. (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res., 40, D130-D135.
27. Rosario, K. et al. (2009) Metagenomic analysis of viruses in reclaimed water. Environ. Microbiol., 11, 2806-2820.
28. Schmieder, R. and Edwards, R. (2011a) Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One, 6, e17288.
29. Schmieder, R. and Edwards, R. (2011b) Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27, 863-864.
30. Schmieder, R. et al. (2010) TagCleaner: identification and removal of tag sequences from genomic and metagenomic datasets. BMC Bioinformatics, 11, 341.
31. Soding, J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics, 21, 951-960.
32. Trindade-Silva, A.E. et al. (2012) Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis. PLoS One, 7, e39905.
33. Willner, D. et al. (2009) Metagenomic signatures of 86 microbial and viral metagenomes. Environ. Microbiol., 11, 1752-1766.
34. Wootters, W.K. (1981) Statistical distance and Hilbert space. Phys. Rev. D, 23, 357-362.
35. Zerbino, D.R. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829.