http://www.oxfordjournals.org/our_journals/bioinformatics/nextgenerationsequencing.html
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 da
Brian On
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 expr
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 da
Takehiro Hashimoto et al.
Bioinformatics (2009) 25: 2613-4 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 Da
Nava Whiteford et al.
Advanced Access publication: 23 June 2009 Full Text
TagDust - A program to eliminate artifacts from next generation sequencing da
Timo Lassmann et al.
Bioinformatics (2009) 25: 2839–2840 Full Text
CDS Prediction
FrameDP: sensitive peptide detection on noisy matured sequences
Jér?me 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 da
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 da
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 da
Geoffrey Faulkner et al.
Advanced Access publication: 15 July 2009 Full Text
Pipeline
PIQA: Pipeline for Illumina G1 Genome Analyzer Da
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 da
Martin Morgan et al.
Advanced Access publication: 3 August 2009 Full Text
RNA-Seq
Statistical Inferences for Isoform Expr
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 da
Nicole Cloonan et al.
Bioinformatics (2009) 25: 2615-6 Full Text
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