RPAN: rice pan-genome browser for ∼3000 rice genomes

An interactive genome browser of association results from the UK10K cohorts project

(2015) Matthias Geihs et al.   BIOINFORMATICS

PopGeV: a web-based large-scale population genome browser: Fig. 1.

(2015) Xinyi Shi et al.   BIOINFORMATICS

Pan-Tetris: an interactive visualisation for Pan-genomes

(2015) André Hennig et al.   BMC BIOINFORMATICS

Ten years of pan-genome analyses

(2015) George Vernikos et al.   CURRENT OPINION IN MICROBIOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface

(2014) Julien Lajugie et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

GPAC—Genome Presence/Absence Compiler: A Web Application to Comparatively Visualize Multiple Genome-Level Changes

(2014) Angela Noll et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

SNP-Seek database of SNPs derived from 3000 rice genomes

(2014) Nickolai Alexandrov et al.   NUCLEIC ACIDS RESEARCH

Insights into the Maize Pan-Genome and Pan-Transcriptome

(2014) C. N. Hirsch et al.   PLANT CELL

The 3,000 rice genomes project

(2014)   GigaScience

JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison

(2013) Phillip Seitzer et al.   BMC BIOINFORMATICS

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

(2013) Hiroaki Sakai et al.   PLANT AND CELL PHYSIOLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Overexpression of OsHsp17.0 and OsHsp23.7 enhances drought and salt tolerance in rice

(2012) Jie Zou et al.   JOURNAL OF PLANT PHYSIOLOGY

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A Major QTL, Ghd8, Plays Pleiotropic Roles in Regulating Grain Productivity, Plant Height, and Heading Date in Rice

(2010) Wen-Hao Yan et al.   Molecular Plant

DTH8 Suppresses Flowering in Rice, Influencing Plant Height and Yield Potential Simultaneously

(2010) X. Wei et al.   PLANT PHYSIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

Building the sequence map of the human pan-genome

(2009) Ruiqiang Li et al.   NATURE BIOTECHNOLOGY

The 1001 Genomes Project for Arabidopsis thaliana

(2009) Detlef Weigel et al.   GENOME BIOLOGY

Identification, characterization and interaction of HAP family genes in rice

(2008) Thiruvengadam Thirumurugan et al.   MOLECULAR GENETICS AND GENOMICS

1000 Genomes project

(2008) Nayanah Siva   NATURE BIOTECHNOLOGY