Comparison of Read Mapping and Variant Calling Tools for the Analysis of Plant NGS Data

Structural variants in 3000 rice genomes

(2019) Roven Rommel Fuentes et al.   GENOME RESEARCH

A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set

(2019) Boas Pucker et al.   PLoS One

Benchmarking variant identification tools for plant diversity discovery

(2019) Xing Wu et al.   BMC GENOMICS

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

(2018) Qiang Zhao et al.   NATURE GENETICS

Comparing the performance of selected variant callers using synthetic data and genome segmentation

(2018) Xiaopeng Bian et al.   BMC BIOINFORMATICS

Rapid gene identification in sugar beet using deep sequencing of DNA from phenotypic pools selected from breeding panels

(2016) David Ries et al.   BMC GENOMICS

From next-generation resequencing reads to a high-quality variant data set

(2016) S P Pfeifer   HEREDITY

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

(2016) Zhongwu Lai et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data

(2016) Anne Bruun Krøigård et al.   PLoS One

A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny

(2016) Boas Pucker et al.   PLoS One

Alignment of Next-Generation Sequencing Reads

(2015) Knut Reinert et al.   Annual Review of Genomics and Human Genetics

The Structural Features of Thousands of T-DNA Insertion Sites Are Consistent with a Double-Strand Break Repair-Based Insertion Mechanism

(2015) Nils Kleinboelting et al.   Molecular Plant

Systematic comparison of variant calling pipelines using gold standard personal exome variants

(2015) Sohyun Hwang et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

Evaluation and Comparison of Multiple Aligners for Next-Generation Sequencing Data Analysis

(2014) Jing Shang et al.   Biomed Research International

Mapping-by-sequencing accelerates forward genetics in barley

(2014) Martin Mascher et al.   GENOME BIOLOGY

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

(2013) S. Pabinger et al.   BRIEFINGS IN BIOINFORMATICS

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

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

(2013) Xiangtao Liu et al.   PLoS One

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

(2013) Matteo Fumagalli   PLoS One

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq)

(2012) Sanzhen Liu et al.   PLoS One

How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?

(2012) Xiaoqing Yu et al.   BioData Mining

Comparative analysis of algorithms for next-generation sequencing read alignment

(2011) M. Ruffalo et al.   BIOINFORMATICS

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

htSeqTools: high-throughput sequencing quality control, processing and visualization in R

(2011) Evarist Planet et al.   BIOINFORMATICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data

(2011) Zhi Wei et al.   NUCLEIC ACIDS RESEARCH

SAMStat: monitoring biases in next generation sequencing data

(2010) T. Lassmann et al.   BIOINFORMATICS

NGSQC: cross-platform quality analysis pipeline for deep sequencing data

(2010) Manhong Dai et al.   BMC GENOMICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

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

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

The 1001 Genomes Project for Arabidopsis thaliana

(2009) Detlef Weigel et al.   GENOME BIOLOGY