Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
作者： Amnon Amir , Daniel McDonald , Jose A. Navas-Molina , Evguenia Kopylova , James T. Morton
DOI: 10.1128/MSYSTEMS.00191-16
关键词:
摘要: … -generation sequencing of the 16S rRNA gene on Illumina … way of running UNOISE2 (ie, we did not run it on the full data set); … to either method were from increased numbers of artifacts, …
scilit.net参考文章(21)
Les Dethlefsen, Sue Huse, Mitchell L Sogin, David A Relman, The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing PLoS Biology. ,vol. 6, pp. e280- ,(2008) , 10.1371/JOURNAL.PBIO.0060280
S Altschula, Warren Gisha, Webb Millerb, E Meyersc, D Lipmana, None, Basic Local Alignment Search Tool Journal of Molecular Biology. ,vol. 215, pp. 403- 410 ,(1990) , 10.1016/S0022-2836(05)80360-2
A Murat Eren, Hilary G Morrison, Pamela J Lescault, Julie Reveillaud, Joseph H Vineis, Mitchell L Sogin, Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. The ISME Journal. ,vol. 9, pp. 968- 979 ,(2015) , 10.1038/ISMEJ.2014.195
Christopher Quince, Anders Lanzen, Russell J Davenport, Peter J Turnbaugh, Removing noise from pyrosequenced amplicons. BMC Bioinformatics. ,vol. 12, pp. 38- 38 ,(2011) , 10.1186/1471-2105-12-38
Jack A Gilbert, Janet K Jansson, Rob Knight, The Earth Microbiome project: successes and aspirations BMC Biology. ,vol. 12, pp. 69- 69 ,(2014) , 10.1186/S12915-014-0069-1
Robert C. Edgar, Search and clustering orders of magnitude faster than BLAST Bioinformatics. ,vol. 26, pp. 2460- 2461 ,(2010) , 10.1093/BIOINFORMATICS/BTQ461
TRAVIS C. GLENN, Field guide to next‐generation DNA sequencers Molecular Ecology Resources. ,vol. 11, pp. 759- 769 ,(2011) , 10.1111/J.1755-0998.2011.03024.X
Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, J Gregory Caporaso, The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome GigaScience. ,vol. 1, pp. 7- 7 ,(2012) , 10.1186/2047-217X-1-7
Robert C. Edgar, Brian J. Haas, Jose C. Clemente, Christopher Quince, Rob Knight, UCHIME improves sensitivity and speed of chimera detection Bioinformatics. ,vol. 27, pp. 2194- 2200 ,(2011) , 10.1093/BIOINFORMATICS/BTR381
Jai Ram Rideout, Yan He, Jose A. Navas-Molina, William A. Walters, Luke K. Ursell, Sean M. Gibbons, John Chase, Daniel McDonald, Antonio Gonzalez, Adam Robbins-Pianka, Jose C. Clemente, Jack A. Gilbert, Susan M. Huse, Hong-Wei Zhou, Rob Knight, J. Gregory Caporaso, Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ. ,vol. 2, ,(2014) , 10.7717/PEERJ.545