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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