4.7 Article

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemical Research Methods

Methods for automatic reference trees and multilevel phylogenetic placement

Lucas Czech et al.

BIOINFORMATICS (2019)

Article Evolutionary Biology

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

Pierre Barbera et al.

SYSTEMATIC BIOLOGY (2019)

Article Biochemical Research Methods

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

Alexey M. Kozlov et al.

BIOINFORMATICS (2019)

Article Biochemistry & Molecular Biology

The European Nucleotide Archive in 2018

Peter W. Harrison et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

Rolf Henrik Nilsson et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

GenBank

Dennis A. Benson et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples

Iliana Bista et al.

MOLECULAR ECOLOGY RESOURCES (2018)

Article Biochemistry & Molecular Biology

A fungal mock community control for amplicon sequencing experiments

Matthew G. Bakker

MOLECULAR ECOLOGY RESOURCES (2018)

Article Multidisciplinary Sciences

Singularity: Scientific containers for mobility of compute

Gregory M. Kurtzer et al.

PLOS ONE (2017)

Article Biochemistry & Molecular Biology

OBITOOLS: a UNIX-inspired software package for DNA metabarcoding

Frederic Boyer et al.

MOLECULAR ECOLOGY RESOURCES (2016)

Article Biotechnology & Applied Microbiology

Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities

Ian M. Bradley et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2016)

Article Biotechnology & Applied Microbiology

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

Daryl M. Gohl et al.

NATURE BIOTECHNOLOGY (2016)

Article Multidisciplinary Sciences

VSEARCH: a versatile open source tool for metagenomics

Torbjorn Rognes et al.

Article Biodiversity Conservation

Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity

Philip Francis Thomsen et al.

BIOLOGICAL CONSERVATION (2015)

Article Multidisciplinary Sciences

Swarm v2: highly-scalable and high-resolution amplicon clustering

Frederic Mahe et al.

Article Biochemical Research Methods

BigDataScript: a scripting language for data pipelines

Pablo Cingolani et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Multidisciplinary Sciences

Swarm: robust and fast clustering method for amplicon-based studies

Frederic Mahe et al.

Article Microbiology

LotuS: an efficient and user-friendly OTU processing pipeline

Falk Hildebrand et al.

MICROBIOME (2014)

Article Biotechnology & Applied Microbiology

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

Sergey I. Nikolenko et al.

BMC GENOMICS (2013)

Article Biochemistry & Molecular Biology

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Christian Quast et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemical Research Methods

PANDAseq: PAired-eND Assembler for Illumina sequences

Andre P. Masella et al.

BMC BIOINFORMATICS (2012)

Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Review Biochemistry & Molecular Biology

Bioinformatic challenges for DNA metabarcoding of plants and animals

Eric Coissac et al.

MOLECULAR ECOLOGY (2012)

Article Multidisciplinary Sciences

CREST - Classification Resources for Environmental Sequence Tags

Anders Lanzen et al.

PLOS ONE (2012)

Article Biochemical Research Methods

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

Xiaolin Hao et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

Search and clustering orders of magnitude faster than BLAST

Robert C. Edgar

BIOINFORMATICS (2010)

Article Biotechnology & Applied Microbiology

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Patrick D. Schloss et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

Article Biotechnology & Applied Microbiology

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

Qiong Wang et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)

Article Biochemistry & Molecular Biology

BOLD: The Barcode of Life Data System (www.barcodinglife.org)

Sujeevan Ratnasingham et al.

MOLECULAR ECOLOGY NOTES (2007)

Article Biochemical Research Methods

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

Ivica Letunic et al.

BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

K Katoh et al.

NUCLEIC ACIDS RESEARCH (2002)