Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys (Q35144953)

6 August 2017

title

Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys (English)

1 reference

6 August 2017

1 reference

2

1 reference

6 August 2017

Michael C Nelson

1

0 references

Joerg Graf

object named as

Joerg Graf

series ordinal

5

0 references

author name string

Jacquelynn Benjamino

series ordinal

3

1 reference

6 August 2017

Sharon L Grim

series ordinal

4

1 reference

6 August 2017

language of work or name

English

0 references

publication date

10 April 2014

1 reference

6 August 2017

1 reference

6 August 2017

volume

9

1 reference

6 August 2017

issue

4

1 reference

6 August 2017

page(s)

e94249

1 reference

Creative Commons Attribution 4.0 International

6 August 2017

copyright license

start time

10 April 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

A filtering method to generate high quality short reads using illumina paired-end technology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Microbial communities in the subglacial waters of the Vatnajökull ice cap, Iceland

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Evaluation of 16S rDNA-based community profiling for human microbiome research

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

A framework for human microbiome research

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

UCHIME improves sensitivity and speed of chimera detection

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

A meta-analysis of the microbial diversity observed in anaerobic digesters

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Microbiome profiling by illumina sequencing of combinatorial sequence-tagged PCR products

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Bacterial community variation in human body habitats across space and time

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Accurate determination of microbial diversity from 454 pyrosequencing data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Accuracy and quality of massively parallel DNA pyrosequencing

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Microbial diversity in the deep sea and the underexplored "rare biosphere"

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Culture-independent characterization of the digestive-tract microbiota of the medicinal leech reveals a tripartite symbiosis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Obesity alters gut microbial ecology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Differential amplification of rRNA genes by polymerase chain reaction

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Updating benchtop sequencing performance comparison

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Performance comparison of benchtop high-throughput sequencing platforms

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Illumina-based analysis of microbial community diversity

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Strategy for microbiome analysis using 16S rRNA gene sequence analysis on the Illumina sequencing platform

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

QIIME allows analysis of high-throughput community sequencing data

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Experimental factors affecting PCR-based estimates of microbial species richness and evenness.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

A core gut microbiome in obese and lean twins

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Characterization of the digestive-tract microbiota of Hirudo orientalis, a european medicinal leech.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Improved extraction of PCR-quality community DNA from digesta and fecal samples

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3983156

10.1371/JOURNAL.PONE.0094249

27 September 2018

Identifiers

DOI

1 reference

6 August 2017

0 references

1 reference

6 August 2017

1 reference