Optimal sequencing depth design for whole genome re-sequencing in pigs

Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length

(2018) Dharminder Bhatia et al.   EUPHYTICA

Sensitivity to sequencing depth in single-cell cancer genomics

(2018) João M. Alves et al.   Genome Medicine

GeneImp: Fast Imputation to Large Reference Panels Using Genotype Likelihoods from Ultralow Coverage Sequencing

(2017) Athina Spiliopoulou et al.   GENETICS

Optimal sequencing strategies for identifying disease-associated singletons

(2017) Sara Rashkin et al.   PLoS Genetics

GeneImp: Fast Imputation to Large Reference Panels Using Genotype Likelihoods from Ultralow Coverage Sequencing

(2017) Athina Spiliopoulou et al.   GENETICS

Impact of sequencing depth and read length on single cell RNA sequencing data of T cells

(2017) Simone Rizzetto et al.   Scientific Reports

Genome-wide genetic variation discovery in Chinese Taihu pig breeds using next generation sequencing

(2016) Z. Wang et al.   ANIMAL GENETICS

Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication

(2016) Ming-Shan Wang et al.   CELL RESEARCH

Rapid genotype imputation from sequence without reference panels

(2016) Robert W Davies et al.   NATURE GENETICS

Identification of genes for controlling swine adipose deposition by integrating transcriptome, whole-genome resequencing, and quantitative trait loci data

(2016) Kai Xing et al.   Scientific Reports

Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds

(2015) Jung-Woo Choi et al.   DNA RESEARCH

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing

(2015) Huashui Ai et al.   NATURE GENETICS

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

Variant Association Tools for Quality Control and Analysis of Large-Scale Sequence and Genotyping Array Data

(2014) Gao T. Wang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genome measures used for quality control are dependent on gene function and ancestry

(2014) Jing Wang et al.   BIOINFORMATICS

Variant calling in low-coverage whole genome sequencing of a Native American population sample

(2014) Chris Bizon et al.   BMC GENOMICS

Population history and genomic signatures for high-altitude adaptation in Tibetan pigs

(2014) Huashui Ai et al.   BMC GENOMICS

Evaluation of variant identification methods for whole genome sequencing data in dairy cattle

(2014) Christine F Baes et al.   BMC GENOMICS

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

(2014) Dylan P. Smith et al.   PLoS One

Reducing INDEL calling errors in whole genome and exome sequencing data

(2014) Han Fang et al.   Genome Medicine

A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly

(2013) Warren R Francis et al.   BMC GENOMICS

Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data

(2013) Aarti Desai et al.   PLoS One

Variant Callers for Next-Generation Sequencing Data: A Comparison Study

(2013) Xiangtao Liu et al.   PLoS One

Optimizing Information in Next-Generation-Sequencing (NGS) Reads for Improving De Novo Genome Assembly

(2013) Tsunglin Liu et al.   PLoS One

Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences

(2013) Matteo Fumagalli   PLoS One

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

(2012)   NATURE

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Strong signatures of selection in the domestic pig genome

(2012) C.-J. Rubin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens

(2011) Ying Wang et al.   BMC BIOINFORMATICS

Low-coverage sequencing: Implications for design of complex trait association studies

(2011) Y. Li et al.   GENOME RESEARCH

Accurate and comprehensive sequencing of personal genomes

(2011) S. S. Ajay et al.   GENOME RESEARCH

Exome and genome analysis as a tool for disease identification and treatment: The 2011 human genome variation society scientific meeting

(2011) William S. Oetting   HUMAN MUTATION

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities

(2011) Matthew N Bainbridge et al.   GENOME BIOLOGY

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

(2010) S. Q. Le et al.   GENOME RESEARCH

Detecting copy number variation with mated short reads

(2010) P. Medvedev et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS