We use cookies to enhance your experience on our website. By continuing to use our website, you are agreeing to our use of cookies. You can change your cookie settings at any time. Find out more Skip to Main Content

Next Generation Sequencing

Next-generation sequencing technologies are revolutionising genomics and their effects are becoming increasingly widespread. Many tools and algorithms relevant to next-generation sequencing applications have been published in Bioinformatics , and so to celebrate this contribution we have gathered these together in this 'Bioinformatics for Next Generation Sequencing' virtual issue. This will be a living resource that we will continually update to include the very latest papers in this area to help researchers keep abreast of the latest developments.

Editorial -Bioinformatics for Next Generation Sequencing

Alex Bateman and John Quackenbush
Bioinformatics (2009) 25 : 429 Full Text

A Report on the 2009 SIG on Short Read Sequencing and Algorithms (Short-SIG)

Michael Brudno et al.
Bioinformatics (2009) 25 : 2863–2864 Full Text

Alignment

Optimal spliced alignments of short sequence reads

Fabio De Bona et al.
Bioinformatics (2008) 24 : i174-80 Full Text

PatMaN: rapid alignment of short sequences to large databases

Kay Prüfer et al.
Bioinformatics (2008) 24 : 1530-1 Full Text
SeqMap: mapping massive amount of oligonucleotides to the genome
Hui Jiang and Wing Wong
Bioinformatics (2008) 24 : 2395-6 Full Text

ZOOM! Zillions of oligos mapped

Hao Lin et al.
Bioinformatics (2008) 24 : 2431-7 Full Text

Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications

Brian Ondov et al.
Bioinformatics (2008) 24 : 2776-7 Full Text

SOAP: short oligonucleotide alignment

Ruiqiang Li et al.
Bioinformatics (2008) 24 : 713-4 Full Text

Annotation of metagenome short reads using Proxygenes

Daniel Dalevi et al.
Bioinformatics (2008) 24 : i7-13 Full Text

Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies

Iman Hajirasouliha
Bioinformatics (2008) 24 : i32-40 Full Text

PASS: a Program to Align Short Sequences

Davide Campagna et al.
Bioinformatics (2009) 25 : 967–968 Full Text

MOM: Maximum Oligonucleotide Mapping

Hugh Eaves and Yuan Gao
Bioinformatics (2009) 25 : 969–970 Full Text

ProbeMatch: Rapid alignment of oligonucleotides to a genome allowing both gaps and mismatches

Jignesh Patel et al.
Advanced Access publication: 7 April 2009 Full Text

Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform

Li Heng and Richard Durbin
Advanced Access publication: 18 May 2009 Full Text

CloudBurst: highly sensitive read mapping with MapReduce

Michael Schatz
Bioinformatics (2009) 25 : 1363–1369 Full Text

SOAP2: an improved ultrafast tool for short read alignment

Ruiqiang Li
Advanced Access publication: 3 June 2009 Full Text

A Fast Hybrid Short Read Fragment Assembly Algorithm

Bertil Schmidt et al.
Advanced Access publication: 17 June 2009 Full Text

PerM: Efficient Mapping of Short Sequencing Reads with Periodic Full Sensitive Spaced Seeds

Yangho Chen et al
Advanced Access publication: 12 August 2009 Full Text

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

Jacob Degner et al.
Advanced Access publication: 6 October 2009 Full Text

Updates to the RMAP short-read mapping software

Andrew Smith et al.
Bioinformatics (2009) 25 : 2841–2842 Full Text

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite

Takehiro Hashimoto et al.
Bioinformatics (2009) 25 : 2613-4 Full Text

Classification of DNA sequences using Bloom filters

Henrik Stranneheim et al.
Bioinformatics (2010) 26: 1595–1600 Full Text

The Sequence Alignment/Map (SAM) Format and SAMtools

Heng Li et al.
Advanced Access publication: 8 June 2009 Full Text

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite

Geoffrey Faulkner et al.
Advanced Access publication: 15 July 2009 Full Text

MicroRazerS: Rapid alignment of small RNA reads

Anne-Katrin Emde et al.
Bioinformatics (2010) 26: 123-124 Full Text

The GNUMAP Algorithm: Unbiased Probabilistic Mapping of Oligonucleotides from Next-Generation Sequencing

Nathan Clement et al.
Bioinformatics (2010) 26: 38-45 Full Text

A Probabilistic Framework for Aligning Paired-end RNA-seq Data

Yin Hu et al.
Advanced Access publication: 23 July 2009 Full Text

An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System

Brain Ondov et al.
Bioinformatics (2010) 26: 1901-1902 Full Text

GASSST: global alignment short sequence search tool

Guillaume Rizk and Dominique Lavenier
Bioinformatics (2010) 26 : 2534–2540 Full Text

Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing

Sanchit Misra et al
Bioinformatics (2011) 27: 189-195 Full Text

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

Thomas Wu and Serban Nacu
Advanced Access publication: 10 February 2010 Full text

RRBSMAP: A Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing

Yuanxin Xi et al
Bioinformatics (2012) 28 : 430-432 Full Text

B-SOLANA: An approach for the analysis of two-base encoding bisulfite sequencing data

Benjamin Kreck et al
Bioinformatics (2012) 28 : 428-429 Full Text

Assembly

Aggressive Assembly of Pyrosequencing Reads with Mates

Jason Miller et al.
Bioinformatics (2008) 24 : 2818-24 Full Text

Assembly reconciliation

Aleskey Zimin et al.
Bioinformatics (2008) 24 : 42-5 Full Text

Consensus Generation and Variant Detection by Celera Assembler

Gennady Denisov et al.
Bioinformatics (2008) 24 : 1035-40 Full Text

Assembling millions of short DNA sequences using SSAKE

Rene Warren et al.
Bioinformatics (2007) 23 : 500-1 Full Text

Extending assembly of short DNA sequences to handle error

William Jeck et al.
Bioinformatics (2007) 23 : 2942-4 Full Text

SCARF: Maximizing next-generation EST assemblies for evolutionary and population genomic analyses

Michael Barker et al.
Bioinformatics (2009) 25 : 535-536 Full Text

Profiling model T-cell metagenomes with short reads

René Warren et al
Bioinformatics (2008) 25 : 458-64 Full Text

A Consistency-based Consensus Algorithm for De Novo and Reference-guided Sequence Assembly of Short Reads.

Tobias Rausch et al.
Bioinformatics (2009) 25 : 1118–1124 Full Text

HI: Haplotype Improver using paired-end short

Quan Long et al.
Advanced Access publication: 1 July 2009 Full Text

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

Kai Ye et al.
Advanced Access publication: 26 June 2009 Full Text

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly

Bas Dutilh et al.
Advanced Access publication: 19 June 2009 Full Text

De novo Transcriptome Assembly with ABySS

Inanc Birol et al.
Advanced Access publication: 15 June 2009 Full Text

Gap5 - editing the billion fragment sequence assembly

James Bonfield and Andrew Whitwham
Advanced Access publication: 30 May 2010 Full text

Efficient construction of an assembly string graph using the FM-index

Jared Simpson and Richard Durbin
Bioinformatics (2010) 26: i367–i373 Full Text

Integrating genome assemblies with MAIA

Jurgen Nijkamp et al
Bioinformatics (2010) 26 : i433–i439 Full Text

Scaffolding pre-assembled contigs using SSPACE

Marten Boetzer et al
Bioinformatics (2011) 27: 578-579 Full Text

Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons

Giuseppe Narzisi and Bud Mishra
Bioinformatics (2011) 27: 153-160 Full Text

QuRe: Software for viral quasispecies reconstruction from next-generation sequencing data

Mattia Prosperi and Marco Salemi
Bioinformatics (2012) 28 : 132-133 Full Text

Graph accordance of next-generation sequence assemblies

Guohui Yao et al
Bioinformatics (2012) 28 : 13-16 Full Text

Fast Scaffolding with Small Independent Mixed Integer Programs

Leena Salmela et al
Bioinformatics (2011) 27 : 3259–3265 Full Text

Bambus 2: Scaffolding Metagenomes

Sergey Koren et al
Bioinformatics (2011) 27 : 2964–2971 Full Text

FLASH: Fast Length Adjustment of Short Reads to Improve Genome Assemblies

Tanga Magoc and Steven Salzberg
Bioinformatics (2011) 27 : 2957-2963 Full Text

Mauve Assembly Metrics

Aaron Darling et al
Bioinformatics (2011) 27 : 2756–2757 Full Text

Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data

Ricardo Ramirez-Gonzalez et al
Bioinformatics (2011) 27 : 2754–2755 Full Text

Paired-end RAD-seq for de-novo assembly and marker design without available reference

Eva-Maria Willing et al
Bioinformatics (2011) 27 : 2187–2193 Full Text

Comparative Studies of de novo Assembly Tools for Next-generation Sequencing Technologies

Yong Lin et al
Bioinformatics (2011) 27 : 2031–2037 Full Text

Meta-IDBA: A de Novo Assembler for Metagenomic Data

Francis Y. L. Chin
Bioinformatics (2011) 27 : i94–i101 Full Text

Base Calling

SHREC: A short-read error correction method

Bertil Schmidt et al.
Advanced Access publication: 19 June 2009 Full Text

Swift: Primary Data Analysis for the Illumina

Nava Whiteford et al.
Advanced Access publication: 23 June 2009 Full Text

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

Timo Lassmann et al.
Bioinformatics (2009) 25 : 2839–2840 Full Text

Correction of sequencing errors in a mixed set of reads

Leena Salmela
Bioinformatics (2010) 26: 1284-1290 Full Text

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

Thomas Otto
Bioinformatics (2010) 26: 1704-1707 Full Text

Reptile: representative tiling for short read error correction

Xiao Yang et al
Bioinformatics (2010) 26 : 2526–2533 Full Text

Transformations for the Compression of FASTQ Quality Scores of Next Generation Sequencing Data

Raymond Wan et al
Advanced Access publication: 13 December 2011 Full Text

CHIP-seq

FindPeaks 3.1: A Tool for Identifying Areas of Enrichment from Massively Parallel Short-Read Sequencing Technology

Anthony Fejes et al.
Bioinformatics (2008) 24 : 1729-30 Full Text

F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags

Alan Boyle et al.
Bioinformatics (2008) 24 : 2537-8 Full Text

Hierarchical Hidden Markov Model with Application to Joint Analysis of ChIP-chip and ChIP-seq data

Hyungwon Choi et al.
Advanced Access publication: 14 May 2009 Ful text

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

Weiqun Peng et al.
Advanced Access publication: 8 June 2009 Full Text

Detecting differential binding of transcription factors with ChIP-seq

Kun Liang and Sunduz Keles
Bioinformatics (2012) 28 : 121-122 Full Text

TIP: A Probabilistic Method for identifying Transcription Factor Target Genes from ChIP-Seq Binding Profiles

Chao Cheng et al
Bioinformatics (2012) 27 : 3221-3227 Full Text

Diagnosis

Statistical Model for Whole Genome Sequencing and Its Application to Minimally Invasive Diagnosis of Fetal Genetic Disease

Tianjiao Chu et al.
Bioinformatics (2009) 25 : 1244–1250 Full Text

ISOLATE: A computational strategy for identifying the primary origin of cancers using high throughput sequencing

Gerald Quon and Quaid Morris
Advanced Access publication: 19 June 2009 Full Text

Identity-By-Descent Filtering of Exome Sequence data for Disease-Gene Identification in Autosomal Recessive Disorders

Christian Rödelsperger et al
Advanced Access publication: 28 January 2011 Full Text

Miscellaneous

FrameDP: sensitive peptide detection on noisy matured sequences

Jérôme Gouzy, Sébastien Carrere and Thomas Schiex
Bioinformatics 25 : 670–671 Full Text

G-SQZ: Compact Encoding of Genomic Sequence and Quality Data

Waibhav Tembe et al
Advanced Access publication: 6 July 2009 Full Text

ART: a next-generation sequencing read simulator

Weichun Huang et al
Advanced Access publication: 23 December 2011 Full text

Detection of microRNAs in color-space

Antonio Marco and Sam Griffiths-Jones
Bioinformatics (2012) 28 : 318-323 Full Text

Identifying small interfering RNA loci from high-throughput sequencing data

Thomas Hardcastle et al
Advanced Access publication: 9 December 2011 Full text

ART: a next-generation sequencing read simulator

Weichun Huang et al
Bioinformatics (2012) 28 : 593–594 Full Text

Pipeline

PIQA: Pipeline for Illumina G1 Genome Analyzer Data Quality Assessment

Antonio Martinez-Alcantara et al.
Advanced Access publication: 14 July 2009 Full Text

ShortRead: A Bioconductor package for input, quality assessment, and exploration of high throughput sequence data

Martin Morgan et al.
Advanced Access publication: 3 August 2009 Full Text

inGAP, an integrated next-gen genome analysis pipeline

Ji Qi et al.
Bioinformatics (2010) 26: 127-139 Full Text

Manipulation of FASTQ data with Galaxy

Daniel Blankenberg et al.
Bioinformatics (2010) 26: 1783-1785 Full Text

GAMES identifies and annotates mutations in next-generation sequencing projects

Maria Elena Sana et al
Advanced Access publication: 22 October 2010 Full text

Manipulation of FASTQ data with Galaxy

Daniel Blankenberg et al
Bioinformatics (2010) 26 : 1783–1785 Full Text

SAMStat: monitoring biases in next generation sequencing data

Timo Lassmann et al
Bioinformatics (2011) 27: 130-131 Full Text

PASSion: A Pattern Growth Algorithm Based Pipeline for Splice Junction Detection in Paired-end RNA-Seq Data

Yanju Zhang et al
Advanced Access publication: 4 January 2012 Full text

MeQA: A pipeline for MeDIP-seq data quality assessment and analysis

Jinyan Huang et al
Advanced Access publication: 22 December 2011 Full text

PGAP: Pan-Genomes Analysis Pipeline

Yongbing Zhao et al
Bioinformatics (2012) 28 : 416-418 Full Text

GenomicTools: a computational platform for developing high-throughput analytics in genomics

Aristotelis Tsirigos et al
Bioinformatics (2012) 28 : 282–283 Full Text

Knime4Bio: a set of custom nodes for the interpretation of Next Generation Sequencing data with KNIME

Pierre Lindenbaum et al
Bioinformatics (2011) 27 : 3200-3201 Full Text

NARWHAL, a primary analysis pipeline for NGS data

Rutger Brouwer
Bioinformatics (2012) 28 : 284-285 Full Text

Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data

Sonja Althammer et al
Bioinformatics (2011) 27 : 3333-3340 Full Text

RNA-Seq

Statistical Inferences for Isoform Expression in RNA-Seq.

Hui Jiang and Wing Wong
Bioinformatics (2009) 25 : 1026–1032 Full Text

A toolkit for analysing large-scale plant small RNA datasets

Simon Moxon et al.
Bioinformatics (2008) 24 : 2252-2253 Full Text

TopHat: discovering splice junctions with RNA-Seq

Cole Trapnell et al.
Bioinformatics (2009) 25 : 1105–1111 Full Text

RNA-MATE: A recursive mapping strategy for high-throughput RNA-sequencing data

Nicole Cloonan et al.
Bioinformatics (2009) 25 : 2615-6 Full Text

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

Likun Wang et al.
Bioinformatics (2010) 26: 136-138 Full Text

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

Jacob Degner et al.
Bioinformatics (2009) 25: 3207-3212 Full Text

Supersplat--spliced RNA-seq alignment

Douglas Bryant Jnr. et al.
Bioinformatics (2010) 26: 1500–1505 Full Text

RNA-Seq gene expression estimation with read mapping uncertainty

Bo Li et al.
Bioinformatics (2010) 26: 518-528 Full Text

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Mark Robinson et al.
Bioinformatics (2010) 26: 139–140 Full Text

Length Bias Correction for RNA-seq Data in Gene Set Analyses

Liyan Gao et al
Bioinformatics (2011) 27: 662–669 Full Text

Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq

Zhengpeng Wu et al
Bioinformatics (2011) 27: 502-508 Full Text

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries

Lukas Habegger et al
Bioinformatics (2011) 27: 281-283 Full Text

htSeqTools: High-Throughput Sequencing Quality Control, Processing and Visualization in R

Evarist Planet et al
Advanced Access publication: 22 December 2011 Full text

Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq

Ming Hu et al
Bioinformatics (2012) 28 : 63-68 Full Text

deepBlockAlign: A tool for aligning RNA-seq profiles of read block patterns

David Langenberger et al
Bioinformatics (2012) 28 : 17-24 Full Text

RNA-Seq Analysis in MeV

Eleanor Howe et al
Bioinformatics (2011) 27 : 3209-3210 Full Text

Variant detection

VarScan: Variant detection in massively parallel

Daniel Koboldt
Advanced Access publication: 19 June 2009 Full Text

SNP-o-matic

Heinrich Manske and Dominic Kwiatkowski
Advanced Access publication: 2 July 2009 Full Text

Slider - Maximum use of probability information for alignment of short sequence reads and SNP detection

Nawar Malhis et al.
Bioinformatics (2009) 25 : 6-13 Full Text

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA

Kathryn Holt et al.
Bioinformatics (2009) 25 : 2074-5 Full Text

Copy number variant detection in inbred strains from short read sequence data

Jared Simpson et al.
Advanced Access publication: 18 December 2009 Full Text

Microindel detection in short-read sequence data

Peter Krawitz er al
Advanced Access publication: 9 February 2010 Full text

SNVMix: predicting single nucleotide variants from next generation sequencing of tumors

Rodrigo Goya et al
Advanced Access publication: 3 February 2010 Full Text

Structural Variation Analysis with Strobe Reads

Anna Ritz et al.
Bioinformatics (2010) 26: 1291-1298 Full Text

Detection of locus and content of novel sequence insertions using paired-end next-generation sequencing

Iman Hajirasouliha et al.
Bioinformatics (2010) 26: 1277-1283 Full Text

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

Iman Hajirasouliha et al.
Bioinformatics (2010) 26: 1277–1283 Full Text

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

Fereydoun Hormozdiari et al.
Bioinformatics (2010) 26: i350–i357 Full Text

VARiD: a variation detection framework for color-space and letter-space platforms

Adrian Dalca et al.
Bioinformatics (2010) 26: i343–i349 Full Text

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

Vikas Bansal
Bioinformatics (2010) 26: i318–i324 Full Text

SLOPE: a quick and accurate method for locating non-SNP structural

Haley Abel et al
Bioinformatics (2010) 26 : 2684–2688 Full Text

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

E. R. Martin et al
Bioinformatics (2010) 26 : 2803–2810 Full Text

SVDetect: a tool to identify genomic structural variations from paired-end

Bruno Zeitouni et al
Bioinformatics (2010) 26 : 1895–1896 Full Text

Next-generation VariationHunter: combinatorial algorithms for transposon

Fereydoun Hormozdiari et aL
Bioinformatics (2010) 26 : i350–i357 Full Text

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

Vikas Bansal
Bioinformatics (2010) 26 : i318-24 Full Text

Detection and characterization of novel sequence insertions using

Iman Hajirasouliha et al
Bioinformatics (2010) 26 : 1277–1283 Full Text

ACCUSA--accurate SNP calling on draft genomes

Sebastian Fröhler and Christoph Dieterich
Bioinformatics (2010) 26 : 1364–1365 Full Text

Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format

Michael Edmonson et al
Advanced Access publication: 28 January 2011 Full Text

MU2A--reconciling the genome and transcriptome to determine the effects of base substitutions

Vijay Garla et al
Bioinformatics (2011) 27: 416–418 Full Text

VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer

Jamie Teer et al
Advanced Access publication: 30 December 2011 Full text

Read Count approach for DNA copy number variants detection

Alberto Magi et al
Advanced Access publication: 23 December 2011 Full text

Control-FREEC: a tool for assessing copy number and allelic content using next generation sequencing data

Valentina Boeva et al
Bioinformatics (2012) 28 : 423–425 Full Text

SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data

Jin Zhang and Yufeng Wu
Bioinformatics (2011) 27 : 3228-3234 Full Text

Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools

Francis San Lucas et al
Bioinformatics (2012) 28 : 421-422 Full Text

TREAT: A Bioinformatics Tool for Variant Annotations and Visualizations in Targeted and Exome Sequencing Data

Yan Asman et al
Bioinformatics (2012) 28 : 277-278 Full Text

SomaticSniper: Identification of Somatic Point Mutations in Whole Genome Sequencing Data

David Larson et al
Bioinformatics (2012) 28 : 311-317 Full Text

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next generation sequence data

Arief Gusnanto et al
Bioinformatics (2012) 28 : 40-47 Full Text

Visualisation

NGSView: an extensible open source editor for next-generation sequencing data

Erik Arner et al.
Bioinformatics (2010) 26: 125-126 Full Text

Tablet – Next Generation Sequence Assembly Visualization

Iain Milne et al.
Advanced Access publication: 4 December 2009 Full Text

CisGenome Browser: A flexible tool for genomic data visualization

Hui Jiang et al.
Advanced Access publication: 30 May 2010 Full text

Savant: Genome Browser for High Throughput Sequencing Data

Marc Flume et al.
Advanced Access publication: 20 June 2010 Full Text

girafe - an R/Bioconductor package for functional exploration of aligned

Joern Toedling et al
Bioinformatics (2010) 26 : 2902–2903 Full Text

Artemis: An integrated platform for visualisation and analysis of high-throughput sequence-based experimental data

Tim Carver et al
Advanced Access publication: 22 December 2011 Full Text

Visualization and quality assessment of de novo genome assemblies

Oksana Riba-Grognuz et al
Bioinformatics (2011) 27 : 3425-3426 Full Text
This Feature Is Available To Subscribers Only

Sign In or Create an Account

This PDF is available to Subscribers Only

View Article Abstract & Purchase Options

For full access to this pdf, sign in to an existing account, or purchase an annual subscription.

Subscribe Now