DUDes: A top-down taxonomic profiler for metagenomics

Bioinformatics

Volumn 32, Issue 15, 2016, Pages 2272-2280

  Piro, Vitor C ^a,b   Lindner, Martin S ^a,c   Renard, Bernhard Y ^a  

^a ROBERT KOCH INSTITUTE   (Germany)

^b MINISTRY OF EDUCATION OF BRAZIL   (Brazil)

^c 4 Antibody AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; GENOME; HIGH THROUGHPUT SEQUENCING; METAGENOMICS;

ALGORITHMS; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOMICS;

EID: 84991517874     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw150     Document Type: Article

References (28)

1. Benson, D.A. et al. (2013) GenBank. Nucleic Acids Res., 41, D36-D42.
2. Brown, C.T. et al. (2012). A reference-free algorithm for computational normalization of shotgun sequencing data. arXiv, 1203.4802, 1-18.
3. Francis, O.E. et al. (2013) Pathoscope: species identification and strain attribution with unassembled sequencing data. Genome Res., 23, 1721-1729.
4. Freitas, T.A.K. et al. (2015) Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Nucleic Acids Res., 43, 1-14.
5. Fricke, W.F. and Rasko, D.A. (2014) Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions. Nat. Rev. Genet., 15, 49-55.
6. Goeman, J.J. and Solari, A. (2014) Multiple hypothesis testing in genomics. Stat. Med., 33, 1946-1978.
7. Handelsmanl, J. et al. (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol., 5, R245-R249.
8. Huson, D.H. et al. (2007) MEGAN analysis of metagenomic data. Genome Res., 17, 377-386.
9. Keeling, P.J. et al. (2014) The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eu-karyotic life in the oceans through transcriptome sequencing. PLoS Biol., 12, e1001889.
10. Klymiuk, I. et al. (2014) A physicians' wish list for the clinical application of intestinal metagenomics. PLoS Med., 11, e1001627.
11. Köser, C.U. et al. (2012) Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog., 8, e1002824.
12. Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
13. Levenshtein, V.I. (1966) Binary codes capable of correcting deletions, insertions, and reversals. Sov. Phys. Dokl., 10, 707-710.
14. Li, H. et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
15. Lindgreen, S. et al. (2016) An evaluation of the accuracy and speed of metage-nome analysis tools. Sci. Rep., 6, 19233.
16. Lindner, M.S. and Renard, B.Y. (2015) Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS. PLoS One, 10, e0117711.
17. Loman, N.J. et al. (2013) A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA, 309, 1502-1510.
18. Mande, S.S. et al. (2012) Classification of metagenomic sequences: Methods and challenges. Brief. Bioinform., 13, 669-681.
19. Meinshausen, N. (2008) Hierarchical testing of variable importance. Biometrika, 95, 265-278.
20. NCBI. (2015) Database resources of the national center for biotechnology information. Nucleic Acids Res., 43, D6.
21. Ounit, R. et al. (2015) CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genomics, 16, 236.
22. Pallen, M.J. (2014) Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections. Parasitology, 141, 1856-1862.
23. Segata, N. et al. (2012) Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods, 9, 811-814.
24. Shakya, M. et al. (2013) Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ. Microbiol., 15, 1882-1899.
25. Sunagawa, S. et al. (2015) Ocean Plankton. Structure and function of the global ocean microbiome. Science, 348, 1261359.
26. Truong, D.T. et al. (2015) MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat. Methods, 12, 902-903.
27. Turnbaugh, P.J. et al. (2007) The human microbiome project. Nature, 449, 804-810.
28. Wood, D.E. and Salzberg, S.L. (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol., 15, R46.