NGmerge: merging paired-end reads via novel empirically-derived models of sequencing errors

Evaluation of Quality Assessment Protocols for High Throughput Genome Resequencing Data

(2017) Matteo Chiara et al.   Frontiers in Genetics

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Culture of previously uncultured members of the human gut microbiota by culturomics

(2016) Jean-Christophe Lagier et al.   Nature Microbiology

Current practices and guidelines for clinical next-generation sequencing oncology testing

(2016) Samuel P. Strom et al.   Cancer Biology & Medicine

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

FlowClus: efficiently filtering and denoising pyrosequenced amplicons

(2015) John M Gaspar et al.   BMC BIOINFORMATICS

High-Throughput Sequencing Technologies

(2015) Jason A. Reuter et al.   MOLECULAR CELL

CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing

(2014) Sunyoung Kwon et al.   BMC BIOINFORMATICS

Navigating the Rapids: The Development of Regulated Next-Generation Sequencing-Based Clinical Trial Assays and Companion Diagnostics

(2014) Saumya Pant et al.   Frontiers in Oncology

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

(2013) J. Zhang et al.   BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

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

(2011) T. Magoc et al.   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

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

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