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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: 28632864 Full Text

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 Prfer 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: 967968 Full Text

MOM: Maximum Oligonucleotide Mapping Hugh Eaves and Yuan Gao Bioinformatics (2009) 25: 969970 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: 13631369 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: 28412842 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: 15951600 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: 25342540 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

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 Ren 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: 11181124 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: i367i373 Full Text

Integrating genome assemblies with MAIA Jurgen Nijkamp et al Bioinformatics (2010) 26: i433i439 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: 32593265 Full Text

Bambus 2: Scaffolding Metagenomes Sergey Koren et al Bioinformatics (2011) 27: 29642971 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: 27562757 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: 27542755 Full Text

Paired-end RAD-seq for de-novo assembly and marker design without available reference Eva-Maria Willing et al Bioinformatics (2011) 27: 21872193 Full Text

Comparative Studies of de novo Assembly Tools for Next-generation Sequencing Technologies Yong Lin et al Bioinformatics (2011) 27: 20312037 Full Text

Meta-IDBA: A de Novo Assembler for Metagenomic Data Francis Y. L. Chin Bioinformatics (2011) 27: i94i101 Full Text

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: 28392840 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: 25262533 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

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

Statistical Model for Whole Genome Sequencing and Its Application to Minimally Invasive Diagnosis of Fetal Genetic Disease Tianjiao Chu et al. Bioinformatics (2009) 25: 12441250 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 Rdelsperger et al Advanced Access publication: 28 January 2011 Full Text

FrameDP: sensitive peptide detection on noisy matured sequences Jrme Gouzy, Sbastien Carrere and Thomas Schiex Bioinformatics 25: 670671 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: 593594 Full Text

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: 17831785 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: 282283 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

Statistical Inferences for Isoform Expression in RNA-Seq. Hui Jiang and Wing Wong Bioinformatics (2009) 25: 10261032 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: 11051111 Full Text

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