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

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

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

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

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

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