Genotype and SNP calling from next-generation sequencing data

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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

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A framework for variation discovery and genotyping using next-generation DNA sequencing data

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dbSNP: the NCBI database of genetic variation

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Sequencing technologies – the next generation

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A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

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SOAP2: an improved ultrafast tool for short read alignment

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ABySS: A parallel assembler for short read sequence dataPreprint

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Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering

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Mapping short DNA sequencing reads and calling variants using mapping quality scores

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A new multipoint method for genome-wide association studies by imputation of genotypes

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The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

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A Block-sorting Lossless Data Compression Algorithm

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Exome sequencing identifies the cause of a mendelian disorder

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A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase

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Score Tests for Association between Traits and Haplotypes when Linkage Phase Is Ambiguous

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Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

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Genotype imputation for genome-wide association studies

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Population genomics of domestic and wild yeasts

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Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

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The sequence and de novo assembly of the giant panda genome

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Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

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SNP detection for massively parallel whole-genome resequencing

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The diploid genome sequence of an Asian individual

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ALLPATHS: de novo assembly of whole-genome shotgun microreads.Preprint

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Evaluation of next generation sequencing platforms for population targeted sequencing studies

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Imputation-Based Analysis of Association Studies: Candidate Regions and Quantitative Traits

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Sense from sequence reads: methods for alignment and assembly

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Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants

Li, Y., Vinckenbosch, N., Tian, G., Huerta‐Sánchez, E., Jiang, T., Jiang, H., Albrechtsen, A., Andersen, G., Cao, H., Korneliussen, T. S., et al. (2010) · Nature Genetics · doi:10.1038/ng.680 · Cited by 307 · see citing works

De novo fragment assembly with short mate-paired reads: Does the read length matter?

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Improved base calling for the Illumina Genome Analyzer using machine learning strategies

Kircher, M., Stenzel, U., & Kelso, J. F. (2009) · Genome biology · doi:10.1186/gb-2009-10-8-r83 · Cited by 271 · see citing works

Quality scores and SNP detection in sequencing-by-synthesis systemsPreprint

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Pyrobayes: an improved base caller for SNP discovery in pyrosequences

Quinlan, A. R., Stewart, D. A., Strömberg, M. P., & Marth, G. (2008) · Nature Methods · doi:10.1038/nmeth.1172 · Cited by 209 · see citing works

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samplesPreprint

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Whole-Genome Sequencing and Assembly with High-Throughput, Short-Read Technologies

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Mapping Trait Loci by Use of Inferred Ancestral Recombination Graphs

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Population genetic analysis of shotgun assemblies of genomic sequences from multiple individualsPreprint

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Accounting for Bias from Sequencing Error in Population Genetic Estimates

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BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencingPreprint

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Design of association studies with pooled or un‐pooled next‐generation sequencing data

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Inference of population genetic parameters in metagenomics: A clean look at messy dataPreprint

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Exome Sequencing of a Multigenerational Human Pedigree

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Multiplex padlock targeted sequencing reveals human hypermutable CpG variationsPreprint

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The Relationship between Imputation Error and Statistical Power in Genetic Association Studies in Diverse Populations

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SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies

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Imputation methods to improve inference in SNP association studies

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Intensity normalization improves color calling in SOLiD sequencing

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naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing

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naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing

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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

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ANGSD: Analysis of Next Generation Sequencing Data

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Genome-wide genetic marker discovery and genotyping using next-generation sequencing

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Benefits and limitations of genome-wide association studies

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A universal SNP and small-indel variant caller using deep neural networks

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Exome sequencing as a tool for Mendelian disease gene discovery

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Robust Demographic Inference from Genomic and SNP Data

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LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

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Dsuite ‐ Fast <i>D</i> ‐statistics and related admixture evidence from VCF files

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An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

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Genotyping‐by‐Sequencing for Plant Breeding and Genetics

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Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

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Transforming clinical microbiology with bacterial genome sequencing

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Genome sequencing and population genomics in non-model organisms

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A high-coverage Neandertal genome from Vindija Cave in Croatia

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Estimating Individual Admixture Proportions from Next Generation Sequencing Data

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Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data

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Haplotype phasing: existing methods and new developments

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Applications of next-generation sequencing to phylogeography and phylogenetics

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CPGView : A package for visualizing detailed chloroplast genome structures

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Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

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A systematic genome-wide analysis of zebrafish protein-coding gene function

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A survey of tools for variant analysis of next-generation genome sequencing data

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Robust Identification of Local Adaptation from Allele Frequencies

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Analysing and interpreting DNA methylation data

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A genomic perspective on hybridization and speciation

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Design and Analysis of Single-Cell Sequencing Experiments

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Big Data Application in Biomedical Research and Health Care: A Literature Review

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Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

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Deriving genotypes from RAD-seq short-read data using Stacks

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RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

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Next generation sequencing and its applications in forensic genetics

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Integrative Analysis of Multi-omics Data for Discovery and Functional Studies of Complex Human Diseases

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SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes

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Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

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A field guide to whole‐genome sequencing, assembly and annotation

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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

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NextGenMap: fast and accurate read mapping in highly polymorphic genomes

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Testing for Hardy–Weinberg Proportions: Have We Lost the Plot?

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Restriction site‐associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference

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Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

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Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

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Haplotype Estimation Using Sequencing Reads

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