High-Quality Reference Genome for an Arid-Adapted Mammal, the Banner-Tailed Kangaroo Rat (Dipodomys spectabilis)

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Life in Deserts: The Genetic Basis of Mammalian Desert Adaptation

(2021) Joana L. Rocha et al.   TRENDS IN ECOLOGY & EVOLUTION

Patterns of genetic partitioning and gene flow in the endangered San Bernardino kangaroo rat (Dipodomys merriami parvus) and implications for conservation management

(2020) Sarah Hendricks et al.   CONSERVATION GENETICS

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Inbreeding load and inbreeding depression estimated from lifetime reproductive success in a small, dispersal-limited population

(2019) Janna R. Willoughby et al.   HEREDITY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Mammalian chromosome–telomere length dynamics

(2018) Amy R. Klegarth et al.   Royal Society Open Science

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic Variation Among Populations of the Endangered Giant Kangaroo Rat, Dipodomys ingens, in the Southern San Joaquin Valley

(2016) Nicole C. Blackhawk et al.   AMERICAN MIDLAND NATURALIST

PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data

(2016) Shenglin Liu et al.   Molecular Ecology Resources

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Natural selection and the genetic basis of osmoregulation in heteromyid rodents as revealed by RNA-seq

(2014) Nicholas J. Marra et al.   MOLECULAR ECOLOGY

A priori and a posteriori approaches for finding genes of evolutionary interest in non-model species: Osmoregulatory genes in the kidney transcriptome of the desert rodent Dipodomys spectabilis (banner-tailed kangaroo rat)

(2012) Nicholas J. Marra et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research

(2012) Meiping Zhang et al.   Nature Protocols

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS