A high-quality Actinidia chinensis (kiwifruit) genome

Chromosome conformation capture resolved near complete genome assembly of broomcorn millet

(2019) Junpeng Shi et al.   Nature Communications

Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping

(2019) Wei Tang et al.   GigaScience

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

(2018) Sarah M. Pilkington et al.   BMC GENOMICS

Draft genome sequence ofCamellia sinensisvar.sinensisprovides insights into the evolution of the tea genome and tea quality

(2018) Chaoling Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis

(2017) En-Hua Xia et al.   Molecular Plant

The draft genome of tropical fruit durian (Durio zibethinus)

(2017) Bin Tean Teh et al.   NATURE GENETICS

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

(2017) Nicolas Daccord et al.   NATURE GENETICS

Rapid radiations of both kiwifruit hybrid lineages and their parents shed light on a two-layer mode of species diversification

(2017) Yifei Liu et al.   NEW PHYTOLOGIST

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Sequencing and de novo assembly of a near complete indica rice genome

(2017) Huilong Du et al.   Nature Communications

Heatmapper: web-enabled heat mapping for all

(2016) Sasha Babicki et al.   NUCLEIC ACIDS RESEARCH

Extensive sequence divergence between the reference genomes of two eliteindicarice varieties Zhenshan 97 and Minghui 63

(2016) Jianwei Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

De Novo Plant Genome Assembly Based on Chromatin Interactions: A Case Study of Arabidopsis thaliana

(2015) Ting Xie et al.   Molecular Plant

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Draft genome of the kiwifruit Actinidia chinensis

(2013) Shengxiong Huang et al.   Nature Communications

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY