Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community.

作者: Robert M. Bowers , Alicia Clum , Hope Tice , Joanne Lim , Kanwar Singh

DOI: 10.1186/S12864-015-2063-6

关键词:

摘要: … low biomass library preparation … library preparation method on library insert size, GC content, community composition, assembly quality and metagenomic binning. We found that library …

参考文章(41)
Meghan Chafee, Loïs Maignien, Sheri L. Simmons, The effects of variable sample biomass on comparative metagenomics Environmental Microbiology. ,vol. 17, pp. 2239- 2253 ,(2015) , 10.1111/1462-2920.12668
Matthew Scholz, Chien-Chi Lo, Patrick S. G. Chain, Improved Assemblies Using a Source-Agnostic Pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of Contigs Scientific Reports. ,vol. 4, pp. 6480- 6480 ,(2015) , 10.1038/SREP06480
Hiroko Yokouchi, Yayoi Fukuoka, Daikichi Mukoyama, Ronie Calugay, Haruko Takeyama, Tadashi Matsunaga, Whole-metagenome amplification of a microbial community associated with scleractinian coral by multiple displacement amplification using phi29 polymerase. Environmental Microbiology. ,vol. 8, pp. 1155- 1163 ,(2006) , 10.1111/J.1462-2920.2006.01005.X
Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette, Jacques Corbeil, Ray Meta: scalable de novo metagenome assembly and profiling Genome Biology. ,vol. 13, pp. 1- 13 ,(2012) , 10.1186/GB-2012-13-12-R122
Suzan Yilmaz, Martin Allgaier, Philip Hugenholtz, Multiple displacement amplification compromises quantitative analysis of metagenomes Nature Methods. ,vol. 7, pp. 943- 944 ,(2010) , 10.1038/NMETH1210-943
Yuval Benjamini, Terence P. Speed, Summarizing and correcting the GC content bias in high-throughput sequencing Nucleic Acids Research. ,vol. 40, ,(2012) , 10.1093/NAR/GKS001
Simone Picelli, Åsa K. Björklund, Björn Reinius, Sven Sagasser, Gösta Winberg, Rickard Sandberg, Tn5 transposase and tagmentation procedures for massively scaled sequencing projects Genome Research. ,vol. 24, pp. 2033- 2040 ,(2014) , 10.1101/GR.177881.114
Genivaldo Gueiros Z. Silva, Daniel A. Cuevas, Bas E. Dutilh, Robert A. Edwards, FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares. PeerJ. ,vol. 2, ,(2014) , 10.7717/PEERJ.425
Robert M. Bowers, Nicholas Clements, Joanne B. Emerson, Christine Wiedinmyer, Michael P. Hannigan, Noah Fierer, Seasonal variability in bacterial and fungal diversity of the near-surface atmosphere. Environmental Science & Technology. ,vol. 47, pp. 12097- 12106 ,(2013) , 10.1021/ES402970S
Sean P Jungbluth, Jana Grote, Huei-Ting Lin, James P Cowen, Michael S Rappé, Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank The ISME Journal. ,vol. 7, pp. 161- 172 ,(2013) , 10.1038/ISMEJ.2012.73