High-throughput estimation of allele frequencies using combined pooled-population sequencing and haplotype-based data processing

Linked‐read sequencing enables haplotype‐resolved resequencing at population scale

(2020) Dave Lutgen et al.   Molecular Ecology Resources

A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction

(2020) Sarah E. Jensen et al.   Plant Genome

Evaluation of variant calling tools for large plant genome re-sequencing

(2020) Zhen Yao et al.   BMC BIOINFORMATICS

Simulation of African and non-African low and high coverage whole genome sequence data to assess variant calling approaches

(2020) Shatha Alosaimi et al.   BRIEFINGS IN BIOINFORMATICS

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination

(2019) Hequan Sun et al.   Nature Communications

Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments

(2019) Susanne Tilk et al.   G3-Genes Genomes Genetics

In vivo insertion pool sequencing identifies virulence factors in a complex fungal–host interaction

(2018) Simon Uhse et al.   PLOS BIOLOGY

A Pooled Sequencing Approach Identifies a Candidate Meiotic Driver inDrosophila

(2017) Kevin H.-C. Wei et al.   GENETICS

How to optimize the precision of allele and haplotype frequency estimates using pooled-sequencing data

(2017) Nicolas O. Rode et al.   Molecular Ecology Resources

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Julia: A Fresh Approach to Numerical Computing

(2017) Jeff Bezanson et al.   SIAM REVIEW

A Pooled Sequencing Approach Identifies a Candidate Meiotic Driver inDrosophila

(2017) Kevin H.-C. Wei et al.   GENETICS

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum

(2017) Aleksey V Zimin et al.   GigaScience

Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data

(2017) Sarah Sandmann et al.   Scientific Reports

Recent Perspective of Next Generation Sequencing: Applications in Molecular Plant Biology and Crop Improvement

(2016) Prashant Yadav et al.   Proceedings of the National Academy of Sciences, India. Section B

Genotyping-by-Sequencing on Pooled Samples and its Use in Measuring Segregation Bias during the Course of Androgenesis in Barley

(2016) Sébastien Bélanger et al.   Plant Genome

Next Generation Sequencing of Pooled Samples: Guideline for Variants’ Filtering

(2016) Santosh Anand et al.   Scientific Reports

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Review of alignment and SNP calling algorithms for next-generation sequencing data

(2015) M. Mielczarek et al.   JOURNAL OF APPLIED GENETICS

Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants

(2015) Aziz Belkadi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data

(2015) Débora Y. C. Brandt et al.   G3-Genes Genomes Genetics

Best practices for evaluating single nucleotide variant calling methods for microbial genomics

(2015) Nathan D. Olson et al.   Frontiers in Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Quantitative group testing-based overlapping pool sequencing to identify rare variant carriers

(2014) Chang-Chang Cao et al.   BMC BIOINFORMATICS

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

High-Throughput Phenotyping to Detect Drought Tolerance QTL in Wild Barley Introgression Lines

(2014) Nora Honsdorf et al.   PLoS One

Comparing a few SNP calling algorithms using low-coverage sequencing data

(2013) Xiaoqing Yu et al.   BMC BIOINFORMATICS

Massive analysis of cDNA Ends (MACE) and miRNA expression profiling identifies proatherogenic pathways in chronic kidney disease

(2013) Adam M Zawada et al.   Epigenetics

Maximum Likelihood Estimation of Frequencies of Known Haplotypes from Pooled Sequence Data

(2013) D. Kessner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping

(2013) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Population genomic footprints of selection and associations with climate in natural populations ofArabidopsis hallerifrom the Alps

(2013) Martin C. Fischer et al.   MOLECULAR ECOLOGY

Accuracy of allele frequency estimation using pooled RNA-Seq

(2013) M. Konczal et al.   Molecular Ecology Resources

Genome Wide Allele Frequency Fingerprints (GWAFFs) of Populations via Genotyping by Sequencing

(2013) Stephen Byrne et al.   PLoS One

Validation of SNP Allele Frequencies Determined by Pooled Next-Generation Sequencing in Natural Populations of a Non-Model Plant Species

(2013) Christian Rellstab et al.   PLoS One

SNP calling by sequencing pooled samples

(2012) Emanuele Raineri et al.   BMC BIOINFORMATICS

A physical, genetic and functional sequence assembly of the barley genome

(2012)   NATURE

Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley

(2012) Jordi Comadran et al.   NATURE GENETICS

Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach

(2012) Jesse A. Poland et al.   PLoS One

Dissection of genetically complex traits with extremely large pools of yeast segregants

(2010) Ian M. Ehrenreich et al.   NATURE

Genome-wide analysis of a long-term evolution experiment with Drosophila

(2010) Molly K. Burke et al.   NATURE

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS