Oxford Journals

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

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

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

SNP-o-matic
Heinrich Manske and Dominic Kwiatkowski
Advanced Access publication: 2 July 2009 Full Text

VarScan: Variant detection in massively parallel
Daniel Koboldt
Advanced Access publication: 19 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

Copy number variant detection in inbred strains from short read sequence data
Jared Simpson et al.
Advanced Access publication: 18 December 2009 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

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

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

CDS Prediction

FrameDP: sensitive peptide detection on noisy matured sequences
Jérôme Gouzy, Sébastien Carrere and Thomas Schiex
Bioinformatics 25: 670–671 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

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

Mapping

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

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

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