Prevention, diagnosis and treatment of high-throughput sequencing data pathologies

On the optimal trimming of high-throughput mRNA sequence data

(2014) Matthew D. MacManes   Frontiers in Genetics

Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

(2013) Meredith L. Carpenter et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Next-Generation Sequencing Platforms

(2013) Elaine R. Mardis   Annual Review of Analytical Chemistry

Tapping the Promise of Genomics in Species with Complex, Nonmodel Genomes

(2013) Candice N. Hirsch et al.   Annual Review of Plant Biology

Mastering methodological pitfalls for surviving the metagenomic jungle

(2013) Tom O. Delmont et al.   BIOESSAYS

Filtering duplicate reads from 454 pyrosequencing data

(2013) Susanne Balzer et al.   BIOINFORMATICS

ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly

(2013) David H. Silver et al.   BIOINFORMATICS

RACER: Rapid and accurate correction of errors in reads

(2013) Lucian Ilie et al.   BIOINFORMATICS

NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets

(2013) Marcus R. Breese et al.   BIOINFORMATICS

Sequencing error correction without a reference genome

(2013) Julie A Sleep et al.   BMC BIOINFORMATICS

HTQC: a fast quality control toolkit for Illumina sequencing data

(2013) Xi Yang et al.   BMC BIOINFORMATICS

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

(2013) Sergey I Nikolenko et al.   BMC GENOMICS

AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads

(2013) Alexis Criscuolo et al.   GENOMICS

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial

(2013) Jochen B. W. Wolf   Molecular Ecology Resources

Of contigs and quagmires: next-generation sequencing pitfalls associated with transcriptomic studies

(2013) J. Andrew DeWoody et al.   Molecular Ecology Resources

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Probabilistic error correction for RNA sequencing

(2013) Hai-Son Le et al.   NUCLEIC ACIDS RESEARCH

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

(2013) Maura Costello et al.   NUCLEIC ACIDS RESEARCH

QC-Chain: Fast and Holistic Quality Control Method for Next-Generation Sequencing Data

(2013) Qian Zhou et al.   PLoS One

Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly

(2013) Yen-Chun Chen et al.   PLoS One

Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

(2013) Nora Rieber et al.   PLoS One

Optimizing Information in Next-Generation-Sequencing (NGS) Reads for Improving De Novo Genome Assembly

(2013) Tsunglin Liu et al.   PLoS One

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

Systematic biases in DNA copy number originate from isolation procedures

(2013) Sebastiaan van Heesch et al.   GENOME BIOLOGY

Reducing assembly complexity of microbial genomes with single-molecule sequencing

(2013) Sergey Koren et al.   GENOME BIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

Improving transcriptome assembly through error correction of high-throughput sequence reads

(2013) Matthew D. MacManes et al.   PeerJ

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

(2013) Sujai Kumar et al.   Frontiers in Genetics

Applications of next-generation sequencing in plant biology

(2012) Ashley N. Egan et al.   AMERICAN JOURNAL OF BOTANY

Fulcrum: condensing redundant reads from high-throughput sequencing studies

(2012) Matthew S. Burriesci et al.   BIOINFORMATICS

SEQanswers: an open access community for collaboratively decoding genomes

(2012) Jing-Woei Li et al.   BIOINFORMATICS

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

(2012) B. Liu et al.   BIOINFORMATICS

pIRS: Profile-based Illumina pair-end reads simulator

(2012) Xuesong Hu et al.   BIOINFORMATICS

Statistical challenges associated with detecting copy number variations with next-generation sequencing

(2012) Shu Mei Teo et al.   BIOINFORMATICS

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data

(2012) Yongchao Liu et al.   BIOINFORMATICS

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC 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

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

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

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Origin of land plants revisited in the light of sequence contamination and missing data

(2012) Simon Laurin-Lemay et al.   CURRENT BIOLOGY

Finished bacterial genomes from shotgun sequence data

(2012) F. J. Ribeiro et al.   GENOME RESEARCH

iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data

(2012) A. M. Mezlini et al.   GENOME RESEARCH

The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis

(2012) Pierre De Wit et al.   Molecular Ecology Resources

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

The expanding scope of DNA sequencing

(2012) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Oxford Nanopore announcement sets sequencing sector abuzz

(2012) Michael Eisenstein   NATURE BIOTECHNOLOGY

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Systematic evaluation of factors influencing ChIP-seq fidelity

(2012) Yiwen Chen et al.   NATURE METHODS

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

(2012) M. Lohse et al.   NUCLEIC ACIDS RESEARCH

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Exploring Pandora's Box: Potential and Pitfalls of Low Coverage Genome Surveys for Evolutionary Biology

(2012) Florian Leese et al.   PLoS One

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

(2012) J. Pell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes

(2012) K. Shiroguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE

(2012) Kevin P. Keegan et al.   PLoS Computational Biology

Quake: quality-aware detection and correction of sequencing errors

(2012) David R Kelley et al.   GENOME BIOLOGY

BIGpre: A Quality Assessment Package for Next-Generation Sequencing Data

(2012) Tongwu Zhang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

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

(2011) T. Magoc et al.   BIOINFORMATICS

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

Addressing challenges in the production and analysis of illumina sequencing data

(2011) Martin Kircher et al.   BMC GENOMICS

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies

(2011) Yong Kong   GENOMICS

Eu-Detect: An algorithm for detecting eukaryotic sequences in metagenomic data sets

(2011) Monzoorul Haque Mohammed et al.   JOURNAL OF BIOSCIENCES

Next-generation sequencing of transcriptomes: a guide to RNA isolation in nonmodel animals

(2011) PHILIPPE GAYRAL et al.   Molecular Ecology Resources

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

PathSeq: software to identify or discover microbes by deep sequencing of human tissue

(2011) Aleksandar D Kostic et al.   NATURE BIOTECHNOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Systematic bias in high-throughput sequencing data and its correction by BEADS

(2011) Ming-Sin Cheung et al.   NUCLEIC ACIDS RESEARCH

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

Abundant Human DNA Contamination Identified in Non-Primate Genome Databases

(2011) Mark S. Longo et al.   PLoS One

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

ConDeTri - A Content Dependent Read Trimmer for Illumina Data

(2011) Linnéa Smeds et al.   PLoS One

Overcoming bias and systematic errors in next generation sequencing data

(2011) Margaret A Taub et al.   Genome Medicine

BioStar: An Online Question & Answer Resource for the Bioinformatics Community

(2011) Laurence D. Parnell et al.   PLoS Computational Biology

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Next generation sequencing in functional genomics

(2010) T. Werner   BRIEFINGS IN BIOINFORMATICS

De novo assembly of short sequence reads

(2010) K. Paszkiewicz et al.   BRIEFINGS IN BIOINFORMATICS

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Next Generation Molecular Ecology

(2010) DIETHARD TAUTZ et al.   MOLECULAR ECOLOGY

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

FRT-seq: amplification-free, strand-specific transcriptome sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

Unlocking Short Read Sequencing for Metagenomics

(2010) Sébastien Rodrigue et al.   PLoS One

Whole exome capture in solution with 3 Gbp of data

(2010) Matthew N Bainbridge et al.   GENOME BIOLOGY

Modeling non-uniformity in short-read rates in RNA-Seq data

(2010) Jun Li et al.   GENOME BIOLOGY

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

TagDust--a program to eliminate artifacts from next generation sequencing data

(2009) T. Lassmann et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

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

Chimeric transcript discovery by paired-end transcriptome sequencing

(2009) C. A. Maher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Harnessing genomics for evolutionary insights

(2009) Antonis Rokas et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2008) Peter C Dolan et al.   BMC BIOINFORMATICS

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

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

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

The impact of next-generation sequencing technology on genetics

(2008) Elaine R. Mardis   TRENDS IN GENETICS

Sequencing breakthroughs for genomic ecology and evolutionary biology

(2007) MATTHEW E. HUDSON   Molecular Ecology Resources