PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform (Q36115589)

12 August 2017

PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform (English)

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12 August 2017

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Hyun S Gweon

1

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Daniel S Read

object named as

Daniel S Read

6

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Robert Griffiths

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Robert I Griffiths

7

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Karsten Schonrogge

object named as

Karsten Schonrogge

8

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author name string

Anna Oliver

2

1 reference

12 August 2017

Joanne Taylor

3

1 reference

12 August 2017

Tim Booth

4

1 reference

12 August 2017

Melanie Gibbs

5

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12 August 2017

25 May 2015

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Methods in Ecology and Evolution

12 August 2017

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12 August 2017

6

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12 August 2017

8

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12 August 2017

973-980

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ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

An Illumina metabarcoding pipeline for fungi

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

Ribosomal Database Project: data and tools for high throughput rRNA analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

From genus to phylum: large-subunit and internal transcribed spacer rRNA operon regions show similar classification accuracies influenced by database composition

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

PEAR: a fast and accurate Illumina Paired-End reAd mergeR.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

Towards a unified paradigm for sequence-based identification of fungi

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

Fungal community analysis by high-throughput sequencing of amplified markers--a user's guide

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

The Fungi: 1, 2, 3 ... 5.1 million species?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

A constructive step towards selecting a DNA barcode for fungi

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

Current state and perspectives of fungal DNA barcoding and rapid identification procedures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

QIIME allows analysis of high-throughput community sequencing data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

The fungal dimension of biological invasions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

Fungal community analysis by large-scale sequencing of environmental samples

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

Fungal high-throughput taxonomic identification tool for use with next-generation sequencing (FHiTINGS).

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

New primers to amplify the fungal ITS2 region--evaluation by 454-sequencing of artificial and natural communities.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

Intraspecific ITS variability in the kingdom fungi as expressed in the international sequence databases and its implications for molecular species identification.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4981123

The fungal dimension of biodiversity: magnitude, significance, and conservation

23 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1111%2F2041-210X.12399

Extensive Fungal Diversity in Plant Roots

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1111%2F2041-210X.12399

21 January 2018

Identifiers

DOI

10.1111/2041-210X.12399

1 reference

12 August 2017

1 reference

12 August 2017

1 reference