Unraveling genomic variation from next generation sequencing data

VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer

(2012) Jamie K. Teer et al.   BIOINFORMATICS

AnnTools: a comprehensive and versatile annotation toolkit for genomic variants

(2012) Vladimir Makarov et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

VAR-MD: A tool to analyze whole exome-genome variants in small human pedigrees with mendelian inheritance

(2012) Murat Sincan et al.   HUMAN MUTATION

A comparison of cataloged variation between International HapMap Consortium and 1000 Genomes Project data

(2012) Carrie C Buchanan et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases

(2012) Miao-Xin Li et al.   NUCLEIC ACIDS RESEARCH

VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era

(2012) Yu-Chang Cheng et al.   NUCLEIC ACIDS RESEARCH

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

(2012) Chengwei Luo et al.   PLoS One

Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease

(2012) Alejandro Sifrim et al.   Genome Medicine

ggbio: an R package for extending the grammar of graphics for genomic data

(2012) Tengfei Yin et al.   GENOME BIOLOGY

SVA: software for annotating and visualizing sequenced human genomes

(2011) Dongliang Ge et al.   BIOINFORMATICS

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

(2011) Yan W. Asmann et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies

(2011) M. C. Schatz et al.   BRIEFINGS IN BIOINFORMATICS

A probabilistic disease-gene finder for personal genomes

(2011) M. Yandell et al.   GENOME RESEARCH

inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data

(2011) Ji Qi et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Prioritizing GWAS Results: A Review of Statistical Methods and Recommendations for Their Application

(2010) Rita M. Cantor et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The GMOD Drupal Bioinformatic Server Framework

(2010) A. Papanicolaou et al.   BIOINFORMATICS

BioRuby: bioinformatics software for the Ruby programming language

(2010) N. Goto et al.   BIOINFORMATICS

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

(2010) Iman Hajirasouliha et al.   BIOINFORMATICS

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

(2010) Fereydoun Hormozdiari et al.   BIOINFORMATICS

G-SQZ: compact encoding of genomic sequence and quality data

(2010) W. Tembe et al.   BIOINFORMATICS

rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data

(2010) Tae-Min Kim et al.   BMC BIOINFORMATICS

SeqAnt: A web service to rapidly identify and annotate DNA sequence variations

(2010) Amol Shetty et al.   BMC BIOINFORMATICS

Genetic Heterogeneity in Human Disease

(2010) Jon McClellan et al.   CELL

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

(2010) A. R. Quinlan et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Visualizing biological data—now and in the future

(2010) Seán I O'Donoghue et al.   NATURE METHODS

Visualizing genomes: techniques and challenges

(2010) Cydney B Nielsen et al.   NATURE METHODS

mrsFAST: a cache-oblivious algorithm for short-read mapping

(2010) Faraz Hach et al.   NATURE METHODS

MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation

(2010) H. Hou et al.   NUCLEIC ACIDS RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The next generation: Using new sequencing technologies to analyse gene regulation

(2010) Rebecca CULLUM et al.   RESPIROLOGY

Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression

(2010) A. Git et al.   RNA

A reference guide for tree analysis and visualization

(2010) Georgios A Pavlopoulos et al.   BioData Mining

Seevolution: visualizing chromosome evolution

(2009) A. Esteban-Marcos et al.   BIOINFORMATICS

Visualization of genomic data with the Hilbert curve

(2009) S. Anders   BIOINFORMATICS

MapView: visualization of short reads alignment on a desktop computer

(2009) H. Bao et al.   BIOINFORMATICS

A geometric approach for classification and comparison of structural variants

(2009) S. Sindi et al.   BIOINFORMATICS

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Genome Projector: zoomable genome map with multiple views

(2009) Kazuharu Arakawa et al.   BMC BIOINFORMATICS

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

(2009) Chao Xie et al.   BMC BIOINFORMATICS

Next generation tools for the annotation of human SNPs

(2009) Rachel Karchin   BRIEFINGS IN BIOINFORMATICS

LookSeq: A browser-based viewer for deep sequencing data

(2009) H. M. Manske et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

ABySS-Explorer: Visualizing Genome Sequence Assemblies

(2009) C.B. Nielsen et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

MizBee: A Multiscale Synteny Browser

(2009) M. Meyer et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

Understanding genome browsing

(2009) Melissa S Cline et al.   NATURE BIOTECHNOLOGY

The UCSC Cancer Genomics Browser

(2009) Jingchun Zhu et al.   NATURE METHODS

MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions

(2009) Seunghak Lee et al.   NATURE METHODS

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

Perspectives and Challenges of Emerging Single-Molecule DNA Sequencing Technologies

(2009) Mingsheng Xu et al.   Small

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

(2009) Jan O Korbel et al.   GENOME BIOLOGY

The 1001 Genomes Project for Arabidopsis thaliana

(2009) Detlef Weigel et al.   GENOME BIOLOGY

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

(2008) Ryan D. Morin et al.   BIOTECHNIQUES

Advantages and limitations of next-generation sequencing technologies: A comparison of electrophoresis and non-electrophoresis methods

(2008) Daniel G. Hert et al.   ELECTROPHORESIS

EagleView: A genome assembly viewer for next-generation sequencing technologies

(2008) W. Huang et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

DHPC: A new tool to express genome structural features

(2008) Xuegong Deng et al.   GENOMICS

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The CGView Server: a comparative genomics tool for circular genomes

(2008) J. R. Grant et al.   NUCLEIC ACIDS RESEARCH

Genetic Mapping in Human Disease

(2008) D. Altshuler et al.   SCIENCE

A survey of visualization tools for biological network analysis

(2008) Georgios A Pavlopoulos et al.   BioData Mining