SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing

A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations

(2016) David Seifert et al.   JOURNAL OF MOLECULAR BIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer

(2016) Alfonso Benítez-Páez et al.   GigaScience

MetAmp: combining amplicon data from multiple markers for OTU analysis

(2015) Ilya Y. Zhbannikov et al.   BIOINFORMATICS

Using Amplicon Deep Sequencing to Detect Genetic Signatures ofPlasmodium vivaxRelapse

(2015) Jessica T. Lin et al.   JOURNAL OF INFECTIOUS DISEASES

Genetic architecture of artemisinin-resistant Plasmodium falciparum

(2015) Olivo Miotto et al.   NATURE GENETICS

Center Variation in Intestinal Microbiota Prior to Late-Onset Sepsis in Preterm Infants

(2015) Diana H. Taft et al.   PLoS One

The vaginal microbiome during pregnancy and the postpartum period in a European population

(2015) David A. MacIntyre et al.   Scientific Reports

Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling

(2014) Stephen J. Salipante et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data

(2014) Adrianto Wirawan et al.   BMC BIOINFORMATICS

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

(2014) Frédéric Mahé et al.   PeerJ

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer

(2013) Sarah-Jane Dawson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Efficient error correction for next-generation sequencing of viral amplicons

(2012) Pavel Skums et al.   BMC BIOINFORMATICS

A survey of error-correction methods for next-generation sequencing

(2012) X. Yang et al.   BRIEFINGS IN BIOINFORMATICS

Fast, accurate error-correction of amplicon pyrosequences using Acacia

(2012) Lauren Bragg et al.   NATURE METHODS

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

(2012) Niko Beerenwinkel et al.   Frontiers in Microbiology

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

(2011) Osvaldo Zagordi et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

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

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

Ultra-deep sequencing for the analysis of viral populations

(2011) Niko Beerenwinkel et al.   Current Opinion in Virology