metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences

Ander C, Schulz-Trieglaff OB, Stoye J, Cox AJ (2013)
BMC Bioinformatics 14(Suppl 5: Proc. of RECOMB-Seq 2013): S2.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
URL
DOI
Autor*in
Ander, ChristinaUniBi; Schulz-Trieglaff, Ole B.; Stoye, JensUniBi ; Cox, Anthony J.
Einrichtung
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Erscheinungsjahr
2013
Zeitschriftentitel
BMC Bioinformatics
Band
14
Ausgabe
Suppl 5: Proc. of RECOMB-Seq 2013
Art.-Nr.
S2
ISSN
1471-2105
Page URI
https://pub.uni-bielefeld.de/record/2575011

Zitieren

Ander C, Schulz-Trieglaff OB, Stoye J, Cox AJ. metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. BMC Bioinformatics. 2013;14(Suppl 5: Proc. of RECOMB-Seq 2013): S2.
Ander, C., Schulz-Trieglaff, O. B., Stoye, J., & Cox, A. J. (2013). metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. BMC Bioinformatics, 14(Suppl 5: Proc. of RECOMB-Seq 2013), S2. doi:10.1186/1471-2105-14-S5-S2
Ander, Christina, Schulz-Trieglaff, Ole B., Stoye, Jens, and Cox, Anthony J. 2013. “metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences”. BMC Bioinformatics 14 (Suppl 5: Proc. of RECOMB-Seq 2013): S2.
Ander, C., Schulz-Trieglaff, O. B., Stoye, J., and Cox, A. J. (2013). metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. BMC Bioinformatics 14:S2.
Ander, C., et al., 2013. metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. BMC Bioinformatics, 14(Suppl 5: Proc. of RECOMB-Seq 2013): S2.
C. Ander, et al., “metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences”, BMC Bioinformatics, vol. 14, 2013, : S2.
Ander, C., Schulz-Trieglaff, O.B., Stoye, J., Cox, A.J.: metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. BMC Bioinformatics. 14, : S2 (2013).
Ander, Christina, Schulz-Trieglaff, Ole B., Stoye, Jens, and Cox, Anthony J. “metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences”. BMC Bioinformatics 14.Suppl 5: Proc. of RECOMB-Seq 2013 (2013): S2.

Link(s) zu Volltext(en)
URL
http://www.biomedcentral.com/content/pdf/1471-2105-14-S5-S2.pdf
Access Level
Restricted Closed Access

5 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

SNPs detection by eBWT positional clustering.
Prezza N, Pisanti N, Sciortino M, Rosone G., Algorithms Mol Biol 14(), 2019
PMID: 30839919
A clinician's guide to microbiome analysis.
Claesson MJ, Clooney AG, O'Toole PW., Nat Rev Gastroenterol Hepatol 14(10), 2017
PMID: 28790452
acdc - Automated Contamination Detection and Confidence estimation for single-cell genome data.
Lux M, Krüger J, Rinke C, Maus I, Schlüter A, Woyke T, Sczyrba A, Hammer B., BMC Bioinformatics 17(1), 2016
PMID: 27998267
Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities.
Peabody MA, Van Rossum T, Lo R, Brinkman FS., BMC Bioinformatics 16(), 2015
PMID: 26537885
A rank-based sequence aligner with applications in phylogenetic analysis.
Dinu LP, Ionescu RT, Tomescu AI., PLoS One 9(8), 2014
PMID: 25133391

23 References

Daten bereitgestellt von Europe PubMed Central.

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO., Nucleic Acids Res. 35(21), 2007
PMID: 17947321
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Wang Q, Garrity GM, Tiedje JM, Cole JR., Appl. Environ. Microbiol. 73(16), 2007
PMID: 17586664
DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences.
Wright ES, Yilmaz LS, Noguera DR., Appl. Environ. Microbiol. 78(3), 2011
PMID: 22101057
A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.
Manichanh C, Chapple CE, Frangeul L, Gloux K, Guigo R, Dore J., Nucleic Acids Res. 36(16), 2008
PMID: 18682527
Environmental genome shotgun sequencing of the Sargasso Sea.
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., Science 304(5667), 2004
PMID: 15001713
The NIH Human Microbiome Project.
NIH HMP Working Group, 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., Genome Res. 19(12), 2009
PMID: 19819907
MEGAN analysis of metagenomic data
AUTHOR UNKNOWN, 2007
Taxonomic classification of metagenomic shotgun sequences with CARMA3.
Gerlach W, Stoye J., Nucleic Acids Res. 39(14), 2011
PMID: 21586583
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Genometa--a fast and accurate classifier for short metagenomic shotgun reads.
Davenport CF, Neugebauer J, Beckmann N, Friedrich B, Kameri B, Kokott S, Paetow M, Siekmann B, Wieding-Drewes M, Wienhofer M, Wolf S, Tummler B, Ahlers V, Sprengel F., PLoS ONE 7(8), 2012
PMID: 22927906
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead B, Trapnell C, Pop M, Salzberg SL., Genome Biol. 10(3), 2009
PMID: 19261174
Fast and accurate short read alignment with Burrows-Wheeler transform.
Li H, Durbin R., Bioinformatics 25(14), 2009
PMID: 19451168
A block sorting data compression algorithm
AUTHOR UNKNOWN, 1994

AUTHOR UNKNOWN, 2008
Opportunistic data structures with applications
AUTHOR UNKNOWN, 2000
NCBI Taxonomy
AUTHOR UNKNOWN, 0
Comparing DNA sequence collections by direct comparison of compressed text indexes
AUTHOR UNKNOWN, 2012
Lightweight BWT construction for very large string collections
AUTHOR UNKNOWN, 2011
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.
Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M., BMC Genomics 12 Suppl 2(), 2011
PMID: 21989143
MetaSim: a sequencing simulator for genomics and metagenomics.
Richter DC, Ott F, Auch AF, Schmid R, Huson DH., PLoS ONE 3(10), 2008
PMID: 18841204
NCBI Microbial Genomes
AUTHOR UNKNOWN, 0
Efficient construction of an assembly string graph using the FM-index.
Simpson JT, Durbin R., Bioinformatics 26(12), 2010
PMID: 20529929
Efficient de novo assembly of large genomes using compressed data structures.
Simpson JT, Durbin R., Genome Res. 22(3), 2011
PMID: 22156294
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 23734710
PubMed | Europe PMC

Suchen in

Google Scholar