Near‐gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research

A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding

(2022) Yun Deng et al.   Molecular Plant

The gap-free potato genome assembly reveals large tandem gene clusters of agronomical importance in highly repeated genomic regions

(2022) Xiaohui Yang et al.   Molecular Plant

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

(2021) Mosè Manni et al.   MOLECULAR BIOLOGY AND EVOLUTION

tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes

(2021) Patricia P Chan et al.   NUCLEIC ACIDS RESEARCH

Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding

(2021) Philipp E. Bayer et al.   Plant Genome

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

(2021) Bo Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement

(2021) Vanika Garg et al.   Journal of Advanced Research

5Gs for crop genetic improvement

(2020) Rajeev K Varshney et al.   CURRENT OPINION IN PLANT BIOLOGY

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

The Arabidopsis leucine‐rich repeat receptor‐like kinase MIK2 is a crucial component of early immune responses to a fungal‐derived elicitor

(2020) Alexander D. Coleman et al.   NEW PHYTOLOGIST

Construction and comparison of three reference‐quality genome assemblies for soybean

(2019) Babu Valliyodan et al.   PLANT JOURNAL

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

(2018) Floréal Cabanettes et al.   PeerJ

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

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

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Molecular and Chromosomal Evidence for Allopolyploidy in Soybean

(2009) N. Gill et al.   PLANT PHYSIOLOGY