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A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

Journal Article · · BMC Genomics
Not Available
Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
ORNL LDRD Director's R&D; USDOE
Grant/Contract Number:
AC05-00OR22725
OSTI ID:
1618593
Alternate ID(s):
OSTI ID: 1265994
Journal Information:
BMC Genomics, Journal Name: BMC Genomics Journal Issue: 1 Vol. 17; ISSN 1471-2164
Publisher:
Springer Science + Business MediaCopyright Statement
Country of Publication:
United Kingdom
Language:
English

References (38)

Considerations for the development and application of control materials to improve metagenomic microbial community profiling journal December 2012
Basic local alignment search tool journal October 1990
Gene capture and random amplification for quantitative recovery of homologous genes journal April 2007
A renaissance for the pioneering 16S rRNA gene journal October 2008
Synthetic microbial communities journal April 2014
Library preparation methods for next-generation sequencing: Tone down the bias journal March 2014
Microbiology: Microbiome science needs a healthy dose of scepticism journal August 2014
Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys journal December 2011
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences journal January 2012
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms journal March 2012
Insights into the phylogeny and coding potential of microbial dark matter journal July 2013
Accurate determination of microbial diversity from 454 pyrosequencing data journal August 2009
Practical innovations for high-throughput amplicon sequencing journal September 2013
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions journal September 2010
Parallel tagged sequencing on the 454 platform journal January 2008
Microbial diversity in the deep sea and the underexplored "rare biosphere" journal July 2006
Fast and accurate short read alignment with Burrows-Wheeler transform journal May 2009
The Sequence Alignment/Map format and SAMtools journal June 2009
Search and clustering orders of magnitude faster than BLAST journal August 2010
SAMStat: monitoring biases in next generation sequencing data journal November 2010
Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics journal January 2011
Large Variations in Bacterial Ribosomal RNA Genes journal March 2012
A quantitative map of nucleotide substitution rates in bacterial rRNA journal September 1996
Short pyrosequencing reads suffice for accurate microbial community analysis journal August 2007
Targeted high-throughput sequencing of tagged nucleic acid samples journal August 2007
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform journal October 2011
Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform journal January 2015
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing journal February 2012
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities: Metagenomic and rRNA diversity characterization journal February 2013
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy journal June 2007
Removing Noise From Pyrosequenced Amplicons journal January 2011
Depauperate genetic variability detected in the American and European bison using genomic techniques journal January 2009
The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing journal February 2007
PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets journal August 2012
The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rRNA Gene Based Diversity Studies journal August 2013
Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys journal April 2014
Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase: Research Reports journal October 2009
Assessing the Accuracy of Quantitative Molecular Microbial Profiling journal November 2014

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