MetaBEETL: High-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences

BMC Bioinformatics

Volumn 14, Issue SUPPL.5, 2013, Pages

  Ander, Christina ^a   Schulz Trieglaff, Ole B ^b   Stoye, Jens ^a   Cox, Anthony J ^b  

^a BIELEFELD UNIVERSITY   (Germany)

^b ILLUMINA INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BURROWS-WHEELER TRANSFORM; COMPUTATIONALLY EFFICIENT; ENVIRONMENTAL PROFILE; HIGH-THROUGHPUT ANALYSIS; MICROBIAL COMMUNITIES; MICROBIAL POPULATIONS; NEXT-GENERATION SEQUENCING; TAXONOMIC COMPOSITION;

DATABASE SYSTEMS; STRAIN;

BACKWARD WAVE TUBES;

ALGORITHM; DNA SEQUENCE; HIGH THROUGHPUT SEQUENCING; HUMAN; METAGENOMICS; MICROBIOLOGY; MICROFLORA; PHYLOGENY; PROCEDURES; ARTICLE; METHODOLOGY;

ALGORITHMS; ENVIRONMENTAL MICROBIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; METAGENOMICS; MICROBIOTA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84876133562     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S5-S2     Document Type: Article

References (23)

1. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007, 35(21):7188-7196. 10.1093/nar/gkm864, 2175337, 17947321.
2. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007, 73(16):5261-5267. 10.1128/AEM.00062-07, 1950982, 17586664.
3. Wright ES, Yilmaz LS, Noguera DR. DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol 2012, 78(3):717-725. 10.1128/AEM.06516-11, 3264099, 22101057.
4. Manichanh C, Chapple CE, Frangeul L, Gloux K, Guigo R, Dore J. A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res 2008, 36(16):5180-5188. 10.1093/nar/gkn496, 2532719, 18682527.
5. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004, 304(5667):66-74. 10.1126/science.1093857, 15001713., http://www.sciencemag.org/content/304/5667/66.abstract
6. Group TNHW, Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, Bonazzi V, McEwen JE, Wetterstrand KA, Deal C, Baker CC, Di Francesco V, Howcroft TK, Karp RW, Lunsford RD, Wellington CR, Belachew T, Wright M, Giblin C, David H, Mills M, Salomon R, Mullins C, Akolkar B, Begg L, Davis C, Grandison L, Humble M, Khalsa J, Little AR, Peavy H, Pontzer C, Portnoy M, Sayre MH, Starke-Reed P, Zakhari S, Read J, Watson B, Guyer M. The NIH Human Microbiome Project. Genome Research 2009, 19(12):2317-2323. 2792171, 19819907., http://genome.cshlp.org/content/19/12/2317.abstract
7. Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Research 2007, 17(3):000., http://genome.cshlp.org/content/early/2007/01/01/gr.5969107.abstract
8. Gerlach W, Stoye J. Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res 2011, 39(14):e91. 10.1093/nar/gkr225, 3152360, 21586583.
9. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Journal of Molecular Biology 1990, 215(3):403-410., http://www.sciencedirect.com/science/article/pii/S0022283605803602
10. Davenport CF, Neugebauer J, Beckmann N, Friedrich B, Kameri B, Kokott S, Paetow M, Siekmann B, Wieding-Drewes M, Wienhöfer M, Wolf S, Tümmler B, Ahlers V, Sprengel F. Genometa - A fast and accurate classifier for short metagenomic shotgun reads. PLoS ONE 2012, 7(8):e41224. 10.1371/journal.pone.0041224, 3424124, 22927906., http://dx.doi.org/10.1371%2Fjournal.pone.0041224
11. Langmead B, Trapnell C, Pop M, Salzberg S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 2009, 10(3):R25+. 2690996, 19261174., http://dx.doi.org/10.1186/gb-2009-10-3-r25
12. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168., http://bioinformatics.oxfordjournals.org/content/25/14/1754.abstract
13. Burrows M, Wheeler DJ. A block sorting data compression algorithm. Tech rep 1994, DIGITAL System Research Center.
14. Adjeroh D, Bell T, Mukherjee A. The Burrows-Wheeler Transform: Data Compression, Suffix Arrays, and Pattern Matching 2008, Springer Publishing Company, Incorporated, 1.
15. Ferragina P, Manzini G. Opportunistic data structures with applications. Proceedings of the 41st Annual Symposium on Foundations of Computer Science 2000, 390-FOCS '00, Washington, DC, USA: IEEE Computer Society., http://dl.acm.org/citation.cfm?id=795666.796543
16. NCBI Taxonomy. , ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy
17. Cox AJ, Jakobi T, Rosone G, Schulz-Trieglaff OB. Comparing DNA sequence collections by direct comparison of compressed text indexes. WABI 2012, Volume 7534 of LNBI 2012, 214-224.
18. Bauer MJ, Cox AJ, Rosone G. Lightweight BWT construction for very large string collections. CPM 2011, Volume 6661 of LNCS 2011, 219-231. Springer.
19. Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics 2011, 12(Suppl 2):S4. 10.1186/1471-2164-12-S2-S4, 3333187, 22369237.
20. Richter DC, Ott F, Auch AF, Schmid R, Huson DH. MetaSim: a sequencing simulator for genomics and metagenomics. PLoS ONE 2008, 3(10):e3373. 10.1371/journal.pone.0003373, 2556396, 18841204.
21. NCBI Microbial Genomes. , ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria
22. Simpson JT, Durbin R. Efficient construction of an assembly string graph using the FM-index. Bioinformatics 2010, 26(12):i367-i373. 10.1093/bioinformatics/btq217, 2881401, 20529929., http://dx.doi.org/10.1093/bioinformatics/btq217
23. Simpson JT, Durbin R. Efficient de novo assembly of large genomes using compressed data structures. Genome Research 2012, 22(3):549-556. 10.1101/gr.126953.111, 3290790, 22156294., http://genome.cshlp.org/content/22/3/549.abstract