IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries (Q35519676)

8 August 2017

IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries (English)

1 reference

8 August 2017

Patricio Jeraldo

1

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Ashutosh Mangalam

object named as

Ashutosh Mangalam

5

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Krishna R Kalari

object named as

Krishna Kalari

2

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author name string

Xianfeng Chen

3

1 reference

8 August 2017

Jaysheel Bhavsar

4

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8 August 2017

Bryan White

6

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8 August 2017

Heidi Nelson

7

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8 August 2017

Jean-Pierre Kocher

8

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8 August 2017

Nicholas Chia

9

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8 August 2017

language of work or name

English

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publication date

15 December 2014

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8 August 2017

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8 August 2017

9

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8 August 2017

12

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8 August 2017

e114804

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Creative Commons Attribution 4.0 International

8 August 2017

start time

15 December 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

phyloseq

object named as

phyloseq

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Diet and exercise orthogonally alter the gut microbiome and reveal independent associations with anxiety and cognition

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Pregnancy's stronghold on the vaginal microbiome

12 July 2018

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Investigating microbial eukaryotic diversity from a global census: insights from a comparison of pyrotag and full-length sequences of 18S rRNA genes

12 July 2018

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Trimmomatic: a flexible trimmer for Illumina sequence data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Infernal 1.1: 100-fold faster RNA homology searches

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

UPARSE: highly accurate OTU sequences from microbial amplicon reads

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Insights into the phylogeny and coding potential of microbial dark matter

12 July 2018

1 reference

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data

12 July 2018

1 reference

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The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

12 July 2018

1 reference

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Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Bioinformatics for the Human Microbiome Project

12 July 2018

1 reference

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Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

The Human Microbiome Project: a community resource for the healthy human microbiome

12 July 2018

1 reference

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

PANDAseq: paired-end assembler for illumina sequences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Illumina-based analysis of microbial community diversity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Robust computational analysis of rRNA hypervariable tag datasets

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Search and clustering orders of magnitude faster than BLAST

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

QIIME allows analysis of high-throughput community sequencing data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Forensic identification using skin bacterial communities

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

FastTree 2--approximately maximum-likelihood trees for large alignments

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

PyNAST: a flexible tool for aligning sequences to a template alignment

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Infernal 1.0: inference of RNA alignments

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

APE: Analyses of Phylogenetics and Evolution in R language

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4266640

The Relation Between the Number of Species and the Number of Individuals in a Random Sample of an Animal Population

12 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0114804

10.1371/JOURNAL.PONE.0114804

21 January 2018

Identifiers

DOI

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8 August 2017

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8 August 2017

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