From next-generation resequencing reads to a high-quality variant data set

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Improvement in detection of minor alleles in next generation sequencing by base quality recalibration

(2016) Shengyu Ni et al.   BMC GENOMICS

Structural variation detection using next-generation sequencing data

(2016) Peiyong Guan et al.   METHODS

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

Alignment of Next-Generation Sequencing Reads

(2015) Knut Reinert et al.   Annual Review of Genomics and Human Genetics

BFC: correcting Illumina sequencing errors

(2015) Heng Li   BIOINFORMATICS

PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm

(2015) Yun-Lung Li et al.   BMC BIOINFORMATICS

VariantMetaCaller: automated fusion of variant calling pipelines for quantitative, precision-based filtering

(2015) András Gézsi et al.   BMC GENOMICS

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction

(2015) David Laehnemann et al.   BRIEFINGS IN BIOINFORMATICS

Accounting for uncertainty in DNA sequencing data

(2015) Jason A. O’Rawe et al.   TRENDS IN GENETICS

An analytical framework for optimizing variant discovery from personal genomes

(2015) Gareth Highnam et al.   Nature Communications

Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype calling accuracy

(2015) M. M. Y. Tin et al.   Molecular Ecology Resources

Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals

(2014) Anthony Youzhi Cheng et al.   BIOINFORMATICS

Trowel: a fast and accurate error correction module for Illumina sequencing reads

(2014) Eun-Cheon Lim et al.   BIOINFORMATICS

Fiona: a parallel and automatic strategy for read error correction

(2014) Marcel H. Schulz et al.   BIOINFORMATICS

BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads

(2014) Yun Heo et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity

(2014) Brandi L Cantarel et al.   BMC BIOINFORMATICS

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data

(2014) Ségolène Caboche et al.   BMC GENOMICS

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications

(2014) Faraz Hach et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Analysis to Improve the Validation Rate for Single Nucleotide Variants Detected by Next-Generation Sequencing

(2014) Mi-Hyun Park et al.   PLoS One

RACER: Rapid and accurate correction of errors in reads

(2013) Lucian Ilie et al.   BIOINFORMATICS

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

(2013) Fritz J. Sedlazeck et al.   BIOINFORMATICS

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets

(2013) Xiao Xu et al.   BMC BIOINFORMATICS

Levenshtein error-correcting barcodes for multiplexed DNA sequencing

(2013) Tilo Buschmann et al.   BMC BIOINFORMATICS

Comparing a few SNP calling algorithms using low-coverage sequencing data

(2013) Xiaoqing Yu et al.   BMC BIOINFORMATICS

Benchmarking short sequence mapping tools

(2013) Ayat Hatem et al.   BMC BIOINFORMATICS

Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

(2013) Matteo Fumagalli et al.   GENETICS

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

(2013) Alexis Criscuolo et al.   GENOMICS

QcReads: An Adapter and Quality Trimming Tool for Next-Generation Sequencing Reads

(2013) Yunfei Ma et al.   Journal of Genetics and Genomics

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

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

TagGD: Fast and Accurate Software for DNA Tag Generation and Demultiplexing

(2013) Paul Igor Costea et al.   PLoS One

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

(2013) Qian Zhou et al.   PLoS One

Variant Callers for Next-Generation Sequencing Data: A Comparison Study

(2013) Xiangtao Liu et al.   PLoS One

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

(2013) Cristian Del Fabbro et al.   PLoS One

Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences

(2013) Matteo Fumagalli   PLoS One

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

(2013) Jason O'Rawe et al.   Genome Medicine

Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

(2012) Goo Jun et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Tools for mapping high-throughput sequencing data

(2012) Nuno A. Fonseca et al.   BIOINFORMATICS

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

(2012) Yongchao Liu et al.   BIOINFORMATICS

ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data

(2012) Christopher R Cabanski et al.   BMC BIOINFORMATICS

An integrative variant analysis suite for whole exome next-generation sequencing data

(2012) Danny Challis et al.   BMC BIOINFORMATICS

Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection

(2012) J. A. Neuman et al.   BRIEFINGS IN BIOINFORMATICS

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

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

BamView: visualizing and interpretation of next-generation sequencing read alignments

(2012) T. Carver et al.   BRIEFINGS IN BIOINFORMATICS

Mapping Reads on a Genomic Sequence: An Algorithmic Overview and a Practical Comparative Analysis

(2012) Sophie Schbath et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Generalized DNA Barcode Design Based on Hamming Codes

(2012) Leonid V. Bystrykh   PLoS One

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

A Comprehensive Evaluation of Alignment Algorithms in the Context of RNA-Seq

(2012) Robert Lindner et al.   PLoS One

Assessing the Accuracy and Power of Population Genetic Inference from Low-Pass Next-Generation Sequencing Data

(2012) Jacob E. Crawford et al.   Frontiers in Genetics

Comparative analysis of algorithms for next-generation sequencing read alignment

(2011) M. Ruffalo et al.   BIOINFORMATICS

Correcting errors in short reads by multiple alignments

(2011) L. Salmela et al.   BIOINFORMATICS

ContEst: estimating cross-contamination of human samples in next-generation sequencing data

(2011) Kristian Cibulskis et al.   BIOINFORMATICS

Error correction of high-throughput sequencing datasets with non-uniform coverage

(2011) P. Medvedev et al.   BIOINFORMATICS

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

SHRiMP2: Sensitive yet Practical Short Read Mapping

(2011) Matei David et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

htSeqTools: high-throughput sequencing quality control, processing and visualization in R

(2011) Evarist Planet et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

(2011) Yongchao Liu et al.   BMC BIOINFORMATICS

A novel and well-defined benchmarking method for second generation read mapping

(2011) Manuel Holtgrewe et al.   BMC BIOINFORMATICS

Estimation of allele frequency and association mapping using next-generation sequencing data

(2011) Su Kim et al.   BMC BIOINFORMATICS

Addressing challenges in the production and analysis of illumina sequencing data

(2011) Martin Kircher et al.   BMC GENOMICS

Inference of Population Mutation Rate and Detection of Segregating Sites from Next-Generation Sequence Data

(2011) Chul Joo Kang et al.   GENETICS

Inference of Site Frequency Spectra From High-Throughput Sequence Data: Quantification of Selection on Nonsynonymous and Synonymous Sites in Humans

(2011) Peter D. Keightley et al.   GENETICS

A Hierarchical Bayesian Model for Next-Generation Population Genomics

(2011) Z. Gompert et al.   GENETICS

ECHO: A reference-free short-read error correction algorithm

(2011) W.-C. Kao et al.   GENOME RESEARCH

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

(2011) Yong Kong   GENOMICS

A decade’s perspective on DNA sequencing technology

(2011) Elaine R. Mardis   NATURE

Integrative genomics viewer

(2011) James T Robinson 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

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

GenomeView: a next-generation genome browser

(2011) T. Abeel et al.   NUCLEIC ACIDS RESEARCH

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura 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

SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data

(2011) Zhi Wei et al.   NUCLEIC ACIDS RESEARCH

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

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

High-throughput DNA sequencing - concepts and limitations

(2010) Martin Kircher et al.   BIOESSAYS

SAMStat: monitoring biases in next generation sequencing data

(2010) T. Lassmann et al.   BIOINFORMATICS

BamView: viewing mapped read alignment data in the context of the reference sequence

(2010) T. Carver et al.   BIOINFORMATICS

Gap5—editing the billion fragment sequence assembly

(2010) James K. Bonfield et al.   BIOINFORMATICS

HiTEC: accurate error correction in high-throughput sequencing data

(2010) L. Ilie et al.   BIOINFORMATICS

Correction of sequencing errors in a mixed set of reads

(2010) L. Salmela   BIOINFORMATICS

A statistical method for the detection of variants from next-generation resequencing of DNA pools

(2010) V. Bansal   BIOINFORMATICS

Savant: genome browser for high-throughput sequencing data

(2010) M. Fiume et al.   BIOINFORMATICS

High quality SNP calling using Illumina data at shallow coverage

(2010) N. Malhis et al.   BIOINFORMATICS

SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies

(2010) E. R. Martin et al.   BIOINFORMATICS

Reptile: representative tiling for short read error correction

(2010) X. Yang et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

SeqTrim: a high-throughput pipeline for preprocessing any type of sequence reads

(2010) Juan Falgueras et al.   BMC BIOINFORMATICS

NGSQC: cross-platform quality analysis pipeline for deep sequencing data

(2010) Manhong Dai et al.   BMC GENOMICS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples

(2010) S. Q. Le et al.   GENOME RESEARCH

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Dindel: Accurate indel calls from short-read data

(2010) C. A. Albers et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware

(2010) Haixiang Shi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

mrsFAST: a cache-oblivious algorithm for short-read mapping

(2010) Faraz Hach et al.   NATURE METHODS

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The $1,000 genome, the $100,000 analysis?

(2010) Elaine R Mardis   Genome Medicine

Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA

(2010) Nils Homer et al.   GENOME BIOLOGY

Detection and correction of false segmental duplications caused by genome mis-assembly

(2010) David R Kelley et al.   GENOME BIOLOGY

SNP-o-matic

(2009) Heinrich Magnus Manske et al.   BIOINFORMATICS

SHREC: a short-read error correction method

(2009) J. Schroder et al.   BIOINFORMATICS

PASS: a program to align short sequences

(2009) D. Campagna et al.   BIOINFORMATICS

MapView: visualization of short reads alignment on a desktop computer

(2009) H. Bao et al.   BIOINFORMATICS

CloudBurst: highly sensitive read mapping with MapReduce

(2009) M. C. Schatz   BIOINFORMATICS

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Estimation of Allele Frequencies From High-Coverage Genome-Sequencing Projects

(2009) M. Lynch   GENETICS

LookSeq: A browser-based viewer for deep sequencing data

(2009) H. M. Manske et al.   GENOME RESEARCH

RazerS--fast read mapping with sensitivity control

(2009) D. Weese et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

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

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

Simultaneous alignment of short reads against multiple genomes

(2009) Korbinian Schneeberger et al.   GENOME BIOLOGY

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

(2009) Martin Kircher et al.   GENOME BIOLOGY

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Using quality scores and longer reads improves accuracy of Solexa read mapping

(2008) Andrew D Smith et al.   BMC BIOINFORMATICS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady 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

Uncertainty in homology inferences: Assessing and improving genomic sequence alignment

(2007) G. Lunter et al.   GENOME RESEARCH