Panoramic: A package for constructing eukaryotic pan‐genomes

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

The genome of Cucurbita argyrosperma (silver-seed gourd) reveals faster rates of protein-coding gene and long noncoding RNA turnover and neofunctionalization within Cucurbita

(2019) Josué Barrera-Redondo et al.   Molecular Plant

ppsPCP: A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline

(2019) Muhammad Tahir ul Qamar et al.   BIOINFORMATICS

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

(2019) Lei Gao et al.   NATURE GENETICS

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana

(2019) Anna-Lena Van de Weyer et al.   CELL

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

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

(2018) Qiang Zhao et al.   NATURE GENETICS

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus

(2018) Bhavna Hurgobin et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

(2018) Jackson Peter et al.   NATURE

Genome graphs and the evolution of genome inference

(2017) Benedict Paten et al.   GENOME RESEARCH

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

panX: pan-genome analysis and exploration

(2017) Wei Ding et al.   NUCLEIC ACIDS RESEARCH

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

(2017) Sean P. Gordon et al.   Nature Communications

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

(2016) Carlos Alonso-Blanco et al.   CELL

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome

(2015) Tanya Z. Berardini et al.   GENESIS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Towards plant pangenomics

(2015) Agnieszka A. Golicz et al.   PLANT BIOTECHNOLOGY JOURNAL

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Personalized Medicine and Human Genetic Diversity

(2014) Y.-F. Lu et al.   Cold Spring Harbor Perspectives in Medicine

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

The First 50 Plant Genomes

(2013) Todd P. Michael et al.   Plant Genome

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Variation of presence/absence genes among Arabidopsis populations

(2012) Shengjun Tan et al.   BMC EVOLUTIONARY BIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS