The Quantification of Representative Sequences pipeline for amplicon sequencing: case study on within-population ITS1 sequence variation in a microparasite infectingDaphnia

High-Throughput Sequencing Characterizes Intertidal Meiofaunal Communities in Northern Gulf of Mexico (Dauphin Island and Mobile Bay, Alabama)

(2016) Pamela M. Brannock et al.   BIOLOGICAL BULLETIN

ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach

(2014) Dimitrios P Lyras et al.   BMC BIOINFORMATICS

Population structure of a microparasite infecting Daphnia: spatio-temporal dynamics

(2014) Justyna Wolinska et al.   BMC EVOLUTIONARY BIOLOGY

An Illumina metabarcoding pipeline for fungi

(2014) Miklós Bálint et al.   Ecology and Evolution

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers

(2013) Gabriel Renaud et al.   BIOINFORMATICS

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

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

(2013) J. Zhang et al.   BIOINFORMATICS

MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout

(2013) Simone Sommer et al.   BMC GENOMICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Capturing the population structure of microparasites: using ITS-sequence data and a pooled DNA approach

(2013) Sabine Giessler et al.   Molecular Ecology Resources

Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?

(2013) Bruce E. Deagle et al.   Molecular Ecology Resources

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi

(2013) Daniel L. Lindner et al.   Ecology and Evolution

Surveying the Microbiome of Ants: Comparing 454 Pyrosequencing with Traditional Methods To Uncover Bacterial Diversity

(2012) Stefanie Kautz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Ultrafast clustering algorithms for metagenomic sequence analysis

(2012) W. Li et al.   BRIEFINGS IN BIOINFORMATICS

Estimation of fungal biomass in forest litter and soil

(2012) Petr Baldrian et al.   Fungal Ecology

|SE|S|AM|E| Barcode: NGS-oriented software for amplicon characterization - application to species and environmental barcoding

(2012) S. PIRY et al.   Molecular Ecology Resources

Structural bias in T4 RNA ligase-mediated 3′-adapter ligation

(2012) Fanglei Zhuang et al.   NUCLEIC ACIDS RESEARCH

Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing

(2012) Sebastian Jünemann et al.   PLoS One

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

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

(2011) B. J. Haas et al.   GENOME RESEARCH

Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness

(2011) Virginia Edgcomb et al.   ISME Journal

Preferential ligation during TA-cloning of multitemplate PCR products — A factor causing bias in microbial community structure analysis

(2011) Márton Palatinszky et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples

(2011) Håvard Kauserud et al.   MYCORRHIZA

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

A Comparison of Parallel Pyrosequencing and Sanger Clone-Based Sequencing and Its Impact on the Characterization of the Genetic Diversity of HIV-1

(2011) Binhua Liang et al.   PLoS One

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

A Daphnia Parasite (Caullerya mesnili) Constitutes a New Member of the Ichthyosporea, a Group of Protists near the Animal-Fungi Divergence

(2010) JENNIFER N. LOHR et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Higher parasite resistance in Daphnia populations with recent epidemics

(2010) C. N. SCHOEBEL et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Transmission mode affects the population genetic structure of Daphnia parasites

(2010) J. WOLINSKA et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences

(2010) Sayed Mohammad Ebrahim Sahraeian et al.   NUCLEIC ACIDS RESEARCH

Statistical Parsimony Networks and Species Assemblages in Cephalotrichid Nemerteans (Nemertea)

(2010) Haixia Chen et al.   PLoS One

Reference-Free Validation of Short Read Data

(2010) Jan Schröder et al.   PLoS One

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

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

THE COST OF BEING COMMON: EVIDENCE FROM NATURALDAPHNIAPOPULATIONS

(2009) Justyna Wolinska et al.   EVOLUTION

Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing

(2009) Magdalena Kröber et al.   JOURNAL OF BIOTECHNOLOGY

The 'rare biosphere': a reality check

(2009) Jens Reeder et al.   NATURE METHODS

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

TileQC: A system for tile-based quality control of Solexa data

(2008) Peter C Dolan et al.   BMC BIOINFORMATICS

Probabilistic base calling of Solexa sequencing data

(2008) Jacques Rougemont et al.   BMC BIOINFORMATICS

Grammar-based distance in progressive multiple sequence alignment

(2008) David J Russell et al.   BMC BIOINFORMATICS

Genetic structure of Heliofungia actiniformis (Scleractinia: Fungiidae) populations in the Indo-Malay Archipelago: implications for live coral trade management efforts

(2008) Leyla Knittweis et al.   CONSERVATION GENETICS

Alta-Cyclic: a self-optimizing base caller for next-generation sequencing

(2008) Yaniv Erlich et al.   NATURE METHODS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH