Twelve years of SAMtools and BCFtools

2021/01/29 by Petr Danecek, James Bonfield, Jennifer Liddle +8 · 708 citations
Biochemistry, Genetics and Molecular Biology · #Gene expression and cancer classification #Genetic Mapping and Diversity in Plants and Animals #Genomics and Phylogenetic Studies

paper · pdf · doi:10.1093/gigascience/giab008

openalex publication_date 2021/01/29 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30

Abstract

BACKGROUND: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. FINDINGS: The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. CONCLUSION: Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.

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• Studying relative RNA localization from nucleus to the cytosol
• Revisiting the species problem in Northeast Pacific ribbon kelp lineages (genus Alaria): Lessons learned using whole genome data
• Investigation of post-vaccinal canine distemper involving the Rockborn-like strain in nine puppies in New Zealand
• Were bed bugs the first urban pest insect? Genome-wide patterns of bed bug demography mirror global human expansion
• Population Genomics Reveals Demographic History and Climate Adaptation in Japanese Arabidopsis halleri
• Genetic regulation of gene expression across multiple tissues in chickens
• The SWI/SNF PBAF complex facilitates REST occupancy at repressive chromatin
• Ancient Microbiomes as Mirrored by DNA Extracted From Century‐Old Herbarium Plants and Associated Soil
• Large Inversions Shape Diversification and Genome Evolution in Common Quails
• Differentiation of European yellow rust subraces within the ‘Warrior(-)’ genetic group
• Cytochrome c oxidase inactivation in Physcomitrium patens reveals that respiration coordinates plant metabolism
• First identification of Cryptosporidium parvum virus 1 (CSpV1) in various subtypes of Cryptosporidium parvum from diarrheic calves, lambs and goat kids from France
• A phased chromosome-level genome of the annelid tubeworm Galeolaria caespitosa
• A benchmark study of compression software for human short-read sequence data
• DNA methylation in the wild: epigenetic transgenerational inheritance can mediate adaptation in clones of wild strawberry (Fragaria vesca)
• Allele age estimators designed for whole-genome datasets show only a moderate reduction in performance when applied to whole-exome datasets
• Environmental DNA Epigenetics Accurately Predicts the Age of Cultured Fish Larvae
• Metagenomic Insights Into the Dietary Diversity of the Adaptive Radiation of Cichlid Fishes in Lake Tanganyika
• Signatures of kin selection in a natural population of the bacteria Bacillus subtilis
• Insights into longhorn beetle (Cerambycidae) evolution from comparative analyses of the red-headed ash borer (Neoclytus acuminatus acuminatus) genome
• Pyrus zhaoxuanii (Rosaceae), A new pear species from Danxiashan Mountain, Guangdong, China
• A structured coalescent model reveals deep ancestral structure shared by all modern humans
• A telomere-to-telomere phased genome of an octoploid strawberry reveals a receptor kinase conferring anthracnose resistance
• Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline
• Genomic basis of adaptation to serpentine soil in two Alyssum species shows convergence with Arabidopsis across 20 million years of divergence
• A single gene orchestrates androgen variation underlying male mating morphs in ruffs
• The genome of the sapphire damselfish Chrysiptera cyanea: a new resource to support further investigation of the evolution of Pomacentrids
• Protective antibodies target cryptic epitope unmasked by cleavage of malaria sporozoite protein
• Abrupt-mediated control of ninjurins regulates Drosophila sessile haemocyte compartments
• Multiple pathways to red carotenoid coloration: House finches ( Haemorhous mexicanus ) do not use CYP2J19 to produce red plumage
• The rapid detection of a neonatal unit outbreak of a wild-type Klebsiella variicola using decentralized Oxford Nanopore sequencing
• Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes
• A genome assembly of the American black bear, Ursus americanus, from California
• Microplastic exposure is associated with epigenomic effects in the model organism Pimephales promelas (fathead minnow)
• Sex chromosome turnover in hybridizing stickleback lineages
• Tissue heterogeneity is associated with phenotypic but not genomic diversity in Wolbachia endosymbionts
• Combined Genomic and Imaging Techniques Show Intense Arsenic Enrichment Caused by Detoxification in a Microbial Mat of the Dead Sea Shore
• First single-strain enrichments of Electrothrix cable bacteria, description of E. aestuarii sp. nov. and E. rattekaaiensis sp. nov., and proposal of a cable bacteria taxonomy following the rules of the SeqCode
• Morphological and genetic evidence suggest gene flow among native and naturalized mint species
• The Drosophila Fab-7 boundary modulates Abd-B gene activity by guiding an inversion of collinear chromatin organization and alternate promoter use
• Low Mutation Load in a Supergene Underpinning Alternative Male Mating Strategies in Ruff (Calidris pugnax)
• Modified meiosis in the tardigrade Hypsibius exemplaris maintains heterozygosity across the genome
• Diversity of Pharmaceuticals Enhances Antibiotic Resistance in the Invertebrate Gut via Biofilm‐Mediated Mechanisms
• Alternate RNA decoding results in stable and abundant proteins in mammals
• Insertion of an invading retrovirus regulates a novel color trait in swordtail fish
• nf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction
• The extra-terminal domain drives the role of BET proteins in transcription
• Modified meiosis in the tardigrade Hypsibius exemplaris maintains heterozygosity across the genome
• Transposable element accumulation drives genome size increase in Hylesia metabus (Lepidoptera: Saturniidae), an urticating moth species from South America
• Why Is It Too Cold? Towards a Mechanistic Understanding of Cold‐Water Pollution Effects on Recruitment of an Imperiled Warmwater Fish
• Collateral sensitivity counteracts the evolution of antifungal drug resistance in Candida auris
• Slab Grave expansion disrupted long co-existence of distinct Bronze Age herders in central Mongolia
• Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts
• A recently evolved TAF8 isoform arising from an Alu insertion increases TFIID assembly complexity in the human lineage
• Ultra-deep sequencing reveals intra-host diversity and co-infection-driven evolution of SARS-CoV-2
• Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase
• Metabolically diverse microorganisms mediating hydrocarbon cycling in the subseafloor sediment of the Challenger Deep
• Comparative Genomics Provide Insight Into the Evolution of European Aphanomyces euteiches Strains
• Deep Sequence Characterization of Tomato Spotted Wilt Virus in Cultivated and Wild-Derived Allotetraploid Peanuts in Georgia, U.S.A.
• Life, the universe, and everything for 42: ultra-low pass sequencing of maize for genotyping, mapping, and pedigree analysis
• A Population Genomics Approach to Understand the Diversity, Migration, and Reproduction of the Rice Pathogen Cercospora janseana
• Mycoheterotrophy and plastid genome evolution in the early-diverging epidendroid orchid tribe Nervilieae: independent transitions in Epipogium and Stereosandra
• Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients
• Living on the Rocks: Genomic Analysis of Limestone Langurs Provides Novel Insights into the Adaptive Evolution in Extreme Karst Environments
• Fungicide Application on Alternate Host Barberry Has Significant Roles in Declining Population Genetic Diversity and the Risk of Emerging New Races of Puccinia striiformis f. sp. tritici
• Segmental copy number amplifications are more stable than aneuploidies in the absence of selection
• Transcriptomic and phenotypic convergence of neurodevelopmental disorder risk genes in vitro and in vivo
• Genetic formation and regional disparities of Kra–Dai and Hmong–Mien speakers inferred from ancient genomes of cave burial populations in southwest China
• Within‐Host Environmental Heterogeneity Is Associated With Phenotypic but Not Genomic Diversity in Wolbachia Endosymbionts
• Joint modeling of whole-genome sequencing data for human height via approximate message passing
• When cells rebel: a comparative genomics investigation into marsupial cancer susceptibility
• Population Genomics of Macrophomina spp. Reveals Cryptic Host Specialization and Evidence for Meiotic Recombination
• An Optimised Method to Identify Reintroduced Swift Foxes ( Vulpes velox ) Through SNP Genotyping of Non‐Invasively Collected Scat Samples Using In‐Solution Hybridisation Capture
• Genomic Evidence for Elevational Segregation and Adaptive Introgression in Prunellidae Radiation
• Chromosome-level genome assembly and methylome profile yield insights for the conservation of endangered loggerhead sea turtles
• Selection shapes the evolution of genome size in a globally invasive plant
• The interplay among space, environment, and gene flow drives genetic differentiation in endemic Baja California Agave sobria subspecies
• Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons
• Meta‐analysis of gonadal transcriptome provides novel insights into sex change mechanism across protogynous fishes
• Space-associated stem cell hallmarks of aging and resilience in astronauts
• Unraveling genome- and immunome-wide genetic diversity in modern and historical Jaguars
• Bacterial Assembly in the Switchgrass Rhizosphere Is Shaped by Phylogeny, Host Genotype, and Growing Site
• Unraveling genetic diversity and population structure of pineapple germplasm using genome-wide SNP markers
• Cas9 Nickase-Mediated Contraction of CAG/CTG Repeats in Vivo is Accompanied by Improvements in Huntington’s Disease Pathology
• The genomic diversity and spatial patterns of Mycobacterium bovis in Ireland revealed by whole genome sequencing
• Genome divergence between European anchovy ecotypes fuelled by structural variants originating from trans-equatorial admixture
• Metagenomics Study of the Commercial Tomato Virome Focused on Virus Species of Epidemiological Interest
• Estimation of genome-wide coupling in rattlesnake hybrids provides insight into the process of speciation and its progress
• Identification, quantification, and elimination of barcode crosstalk in multiplexed Oxford Nanopore sequencing
• HTSlib: C library for reading/writing high-throughput sequencing data
• Spread of a Single Superclone Drives Insecticide Resistance in Acyrthosiphon kondoi Across an Invasive Range
• Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding
• Modtector: Ultra-Fast Modification Signal Mining on Mapped Sequencing Reads
• Chromosome-Level Assembly and Annotation of the Grey Reef Shark (Carcharhinus amblyrhynchos) Genome
• Admixture between lineages of the tramp ant Technomyrmex albipes revealed by mitochondrial and ultra-conserved element sequencing
• A PRDM16-CtBP1/2 complex interacts with HDAC1/2 to regulate transcriptional programs of neurogenesis and guide cortical neuron migration
• Florida scrub-jay genomes across space and time reveal impacts of population decline and reduced gene flow
• Genomic vulnerability to climate change of a poorly dispersing and threatened fish, the southern pygmy perch ( Nannoperca australis )
• Replication-stress-induced chromatin loops protect fork stability
• GRHL and PGR control WNT4 expression via 3D looping of conserved and species-specific enhancers
• Rhododendron jiucaipingensis (Ericaceae), a new species from Guizhou, China
• Adaptive introgression and incompatibility shape interspecific hybrid genomes in ornamental and feral Xiphophorus strains
• Two chromosome-scale genomes of wild Aedes aegypti aegypti mosquitoes from North America and South-East Asia
• CUT&Tag for High‐Resolution Epigenomic Profiling From a Low Amount of Arabidopsis Tissue
• Cooperative reading of DECA-CCAAT composite element by the TALE/NF-Y/Sp2 transcription factors
• Admixture and environment shape population genetic and phytochemical variation across a conifer hybrid zone ( Juniperus , Cupressaceae)
• Paneth-like transition drives resistance to dual targeting of KRAS and EGFR in colorectal cancer
• PanVariants: Best Practice for Pangenome-based Variant Calling Pipeline and Framework
• RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity
• Genome assemblies of two bumble bee species: Bombus sonorus and Bombus vosnesenskii
• A chromosome level genome assembly of the marine flowering plant, Torrey’s surfgrass ( Phyllospadix Torreyi ) reveals an exceptionally large Y-chromosome
• PKL mediates H3K4me2 modification and spatial gene congregation in chromatin regulation
• Metagenomic profiling of airborne microbial communities from aircraft filters and face masks
• Genomic Assessment of Giraffes in North American Collections Highlights Conservation Challenges
• Haplotype-resolved telomere-to-telomere reference genome of sweet cherry 'Tieton’ v3.0 characterized the large fragment deletion associated with yellow-skinned variety
• Host–virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier
• Sickle cell status skews malaria parasite genotype at infection
• Long-read de novo assembly of the spekboom (Portulacaria afra) genome
• Does size matter? The integrated roles of light, adaptive sex expression, and hybridization in a widespread Arisaema (Araceae) species from western Japan
• The Genomic Legacy of the Norman Conquest in Rural England
• ZNF334 truncation mutation drives cold-induced autoinflammation
• A Study on the Response Mechanism of Davidia involucrata Baill. to Drought Stress Based on Transcriptomic Analysis
• Harmonizing genotype array data to understand genetic risk for brain amyloid burden in the AMYPAD PNHS Consortium
• Bovine SNP array-based genetic assessment of American plains bison at American Prairie
• A chromosome-scale genome assembly of Hordeum erectifolium : genomic, transcriptomic and anatomical adaptations to drought in a wild barley relative
• Assessment of genetic diversity in a locally endangered tern species suggests population connection instead of isolation
• Mutations Elevate an Underground Pathway to a Physiologically Relevant Protopathway
• A More Rapid Method for Culturing LUHMES-Derived Neurons Provides Greater Cell Numbers and Facilitates Studies of Multiple Viruses
• Genome assembly of the Antipodean and Gibson’s albatrosses ( Diomedea antipodensis antipodensis and D. a. gibsoni )
• Dissecting genotype-environment relationships with functional implications for parental selection in Cannabis breeding
• Endo180 and basement membrane stiffness induce OXPHOS and neoplastic transformation in aging prostate epithelia
• PVGA: a precise viral genome assembler using an iterative alignment graph
• Genetic history of Scythia
• A reproducible ddRAD-seq protocol reveals novel genomic association signatures for fruit-related traits in peach
• k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance
• Reproductive modes in populations of late-acting self-incompatible and self-compatible polyploid Ludwigia grandiflora subsp. hexapetala in western Europe
• Functional and evolutionary insights into chemosensation and specialized herbivory from the genome of the red milkweed beetle, Tetraopes tetrophthalmus (Cerambycidae: Lamiinae)
• White-Brown switching controls phenotypic plasticity and virulence of Candida auris
• Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample
• Molecular investigation of unexpected Helicobacter pylori bacteremia
• Unraveling evolutionary pathways: allopolyploidization and introgression in polyploid Prunus (Rosaceae)
• Deconstructing the common anteroposterior organisation of adult bilaterian guts
• Chromosome-level reference genome for the medically important Arabian horned viper ( Cerastes gasperettii )
• Genome Structural Variants Shape Adaptive Success of an Invasive Urban Malaria Vector Anopheles stephensi
• Accounting for Chimerism in Demographic Inference: Reconstructing the History of Common Marmosets ( Callithrix jacchus ) from High-Quality, Whole-Genome, Population-Level Data
• M6Allele: a toolkit for detection of allele-specific RNA N6-methyladenosine modifications
• Genomic Analysis of Hair Sheep From West/Central Africa Reveals Unique Genetic Diversity and Ancestral Links to Breed Formation in the Caribbean
• Nanorate sequencing reveals the Arabidopsis somatic mutation landscape
• Population Genomics Provides Insights Into Genomic Features of Inbreeding Depression in Arma Chinensis
• Disruption of HaVipR1 confers Vip3Aa resistance in the moth crop pest Helicoverpa armigera
• Where Did the Y Chromosome in the Spiny Rat Go, and How Did It Get There?
• Cell expansion for notochord mechanics and endochondral bone lengthening in zebrafish depends on the 5′-inositol phosphatase Inppl1a
• Historic Museum Samples Provide Evidence for a Recent Replacement of Wolbachia Types in European Drosophila melanogaster
• A simple method to efficiently generate structural variation in plants
• Identification of a sex-determining locus potentially involved in a conflict over sex-ratio
• Laboratory evolution of the bacterial genome structure through insertion sequence activation
• Plio‐Pleistocene Climatic Fluctuations and Divergence With Gene Flow Drive Continent‐Wide Diversification in an African Bird
• Genes that cause severe liver disease in children also influence risk and severity of common liver conditions in adults
• Distinct genomic contexts predict gene presence–absence variation in different pathotypes of Magnaporthe oryzae
• DNA-guided transcription factor cooperativity shapes face and limb mesenchyme
• Genomic Introgression and Adaptation of Southern Seabird Species Facilitate Recent Polar Colonization
• eDNA metabarcoding and whole genome sequencing detect European-American Eel hybrids in northeastern Canada
• The genome of Vitis vinifera cv. Mgaloblishvili reveals resistance and susceptibility factors to downy mildew in the Rpv29 and Rpv31 loci
• Population genomics of Vitis pseudoreticulata reveals the genetic basis of fungal resistance in grapevine
• Endemic transmission of a Mycobacterium tuberculosis L2.2.M3 sublineage of the L2 lineage within Colon, Panama: A prospective study
• Purging of Highly Deleterious Mutations Through an Extreme Bottleneck
• Plasmid conjugation drives within–patient plasmid diversity
• The role of mating systems in postzygotic reproductive isolation between two recently divergent Aquilegia Species
• Moroccan genome project: genomic insight into a North African population
• Constructing a draft Indian cattle pangenome using short-read sequencing
• Validating a Target‐Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals
• Monitoring biodiversity in the global change era: The importance of herbaria and genetic diversity
• On the impact of reference selection on variant calling in phylogenomics: How to avoid systematic error in target-enrichment studies of non-model organisms
• Identification of Cell Fate Determining Transcription Factors for Generating Brain Endothelial Cells
• First reference genomes for two mesophotic, reef-building coral species: Leptoseris cf. scabra and Montipora cf. grisea
• Asian diversity in human immune cells
• Variable performance of widely used bisulfite sequencing methods and read mapping software for DNA methylation
• Recurrent ERBB2 alterations are associated with esophageal adenocarcinoma brain metastases
• The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired
• Synthesizing environmental, epidemiological and vector and parasite genetic data to assist decision making for disease elimination
• Inhibition of PRC2 enables self-renewal of blastoid-competent naive pluripotent stem cells from chimpanzee
• Chromosome‐level assemblies of Amaranthus palmeri, Amaranthus retroflexus, and Amaranthus hybridus allow for genomic comparisons and identification of a sex‐determining region
• Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility
• Triploidy is prominent in the duckweed Lemna minor complex
• The epigenetic landscape shapes smoking-induced mutagenesis by modulating DNA damage susceptibility and repair efficiency
• Comprehensive Profiling of Computational Techniques for Sequencing‐Based HLA Immune Signatures Extraction
• Exploring DNA degradation in situ and in museum storage through genomics and metagenomics
• Avoidable false PSMC population size peaks occur across numerous studies
• Comparison of kinship‐identification methods for robust stock assessment using close‐kin mark–recapture data for Pacific bluefin tuna
• Establishing a comprehensive web‐based analysis platform for Nicotiana benthamiana genome and transcriptome
• The hybrid history of zebrafish
• The multi-level effect of chlorpyrifos during clownfish metamorphosis
• SapBase: A central portal for functional and comparative genomics of Sapindaceae species
• Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data
• Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific
• An improved chromosome-level genome assembly of perennial ryegrass (Lolium perenne L.)
• Investigating the Evolution of Drosophila STING-Dependent Antiviral Innate Immunity by Multispecies Comparison of 2′3′-cGAMP Responses
• Identification of Novel Quantitative Trait Loci Associated with Table Grape Fruit Quality Characteristics in a Segregating Population and Transferability of Existing Quality Markers
• Reovirus infection induces transcriptome-wide unique A-to-I editing changes in the murine fibroblasts
• De novo genome and transcriptome assembly of Kelletia kelletii, a coastal gastropod and fisheries species exhibiting a northern range expansion
• A reference assembly for the legume cover crop hairy vetch (Vicia villosa)
• Phylogenomic and demographic history of the Cape cliff lizard ( Hemicordylus capensis )
• The Complete Plastid Genome of Astrohibiscus caesius (Hibisceae, Malvaceae) and Its Phylogenetic Placement
• The critical role of the endogenous immune compartment after CAR T cell therapy in recurrent GBM
• De novo assembly of complete Plasmodium falciparum isolate genomes using PacBio HiFi sequencing technology
• The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors
• Divergent cis - regulatory haplotypes at Tlr2 are associated with immune responsiveness
• Deep coalescent history of the hominin lineage
• Large-scale mitogenome analysis reveals complex maternal genetic connections between Sino-Tibetan- and Altaic-speaking populations
• Draft Genome Sequence of Botrytis fabiopsis , a Causal Agent of Chocolate Spot on Broad Bean ( Vicia faba ) Newly Recorded in Japan
• Gene regulation in response to host sex and infection route in Brugia pahangi with new genome annotation
• POU5F1/OCT4 Attenuates Human LINE‐1 Expression Levels in Induced Pluripotent Stem Cells
• Intraspecific neighbourhood effects on male and female fitness in Moricandia moricandioides
• Diversity and Structure of Diaporthe humulicola Populations from Eastern North America
• Mosaic accumulation of somatic genetic variation and estimates of age in the long-lived reef-building coral Acropora palmata
• Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich’s ataxia
• Nicotinamide Adenine Dinucleotide (NAD + ) Induces Defense Responses Against Powdery Mildew and Regulates LecRLK Gene Expression in Squash
• Evolutionary genomics of a natural Wolbachia superinfection in the dengue mosquito Aedes albopictus
• Investigating genetic differentiation between brackish and fresh water collections of the arboviral vector Aedes aegypti
• Beyond chromatin accessibility: bulk ATAC-seq as an integrative assay to portray genomes and epigenomes
• Target capture efficiently resolves the long‐standing taxonomic dead end of Diachrysia moths
• Non-destructive transcriptomics via vesicular export
• The oncogenome of the domestic cat
• Truncation of IFT80 causes early embryonic loss in cattle
• Forest Disturbance Drives Changes in the Functional Traits of Soil Bacteria: A Metagenomic Study of Kauri ( Agathis australis ) Forest Ecosystems
• Signatures of Innovation and Selection in the Extremotolerant Yeast Kluyveromyces marxianus
• Unmasking Tomato Spotted Wilt Virus in Peanuts: From Nucleocapsid Protein Sequence and Localization to Practical Management in Alabama
• Screening metatranscriptomes for ultrastable RNA secondary structures reveals hidden bacteriophages and novel capsid nanomaterials
• Transcriptome profiling reveals divergent response strategies in two olive cultivars with contrasting drought tolerance
• Genome assembly for the Sierra Nevada Parnassian ( Parnassius behrii ) and a brief review of butterfly genome sizes
• Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae
• Archaic Adaptive Introgression in Modern Human Reproductive Genes
• Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield
• Comparative genomics of endemic Staphylococcus aureus ST1 in New Zealand
• Comprehensive Annotation of Olfactory and Gustatory Receptor Genes and Transposable Elements Revealed Their Evolutionary Dynamics in Aphids
• Symbionts with eroded genomes adjust gene expression according to host life-stage and environment
• A draft human pangenome reference
• The role of toxin/antidote genes in the maintenance and evolution of accessory chromosomes in Fusarium
• From constraint to opportunity: Relaxing sexual antagonism reveals adaptive potential maintained by balancing selection
• Conservation and divergence of sex-biased gene expression across 50 million years of Drosophila evolution
• An ancient origin of the naked grains of maize
• Integrative Genotyping and Analysis of Canine Structural Variation Using Long-read and Short-read Data
• Conservation Arks: Genomic Erosion and Inbreeding in an Abundant Island Population of Koalas
• Going deep: phylogenomic analyses incorporating museomic data reveal divergence and character evolution in Decapodiformes (Mollusca: Cephalopoda)
• Whole Mitochondrial Genome Analysis of Killer Whales Reveals the Presence of Resident and Transient Ecotypes Around Hokkaido
• Regulatory landscape of widespread stop codon readthrough in Drosophila
• Dual role of Oct4 and Sox2 in controlling the developmental capacity and timing of tissue morphogenesis in the embryonic lineage
• The Genomic Imprint of Chromosomal Inversions and Demographic History in Island Populations of Deer Mice
• Mapping Species Birth Across the Recombination Landscapes of Marine Snails
• Decentralized nanopore genomics reveals diverse Klebsiella pneumoniae and no evidence of patient–patient transmission in a New Zealand hospital
• Vibrio pectenicida strain FHCF-3 is a causative agent of sea star wasting disease
• Bone Adhered Sediments as a Source of Target and Environmental DNA and Proteins
• Combination of 3D chromatin architecture and omics analysis provides insight into anthocyanin regulation in Actinidia arguta
• The annotated, chromosome-scale Salicornia depressa (American pickleweed) genome
• Evolutionary Consequences of Unusually Large Pericentric TE-rich Regions in the Genome of a Neotropical Fig Wasp
• Microbiome and resistome characterization of patients colonized with carbapenem-resistant Enterobacterales by long-read metagenomic next-generation sequencing of rectal swabs
• Variation in Genome Architecture and Epigenetic Modification Across the Microsporidia Phylogeny
• Seasonal genotypic and phenotypic differentiation of a cosmopolitan freshwater diatom
• Wild genes to the rescue: High-throughput genomics reveals the wild source of broomrape resistance in sunflower
• Multi-omics uncovers transcriptional programs of gut-resident memory CD4+ T cells in Crohn’s disease
• Persistent Genomic Erosion in Whooping Cranes Despite Demographic Recovery
• Characterisation of the Historic Demographic Decline of the British European Polecat Population
• The nature of complex structural variations in tomatoes
• A genome assembly of the California poppy, Eschscholzia californica
• Origin, domestication, and diversity of the climate resilient Ethiopian cereal teff
• The reference genome of a Sierra Nevada endemic, the cut-leaved monkeyflower, Mimulus laciniatus (syn. Erythranthe lacinata )
• Single-cross prediction with imputed multiomic data: a case study in rapeseed
• Ancient origin of an urban underground mosquito
• Effects of Amikacin Liposome Inhalation Suspension and Amikacin Resistance Development in Patients With Refractory Mycobacterium avium Complex Pulmonary Disease
• Fourier transform infrared spectroscopy as a new tool to investigate Clostridioides difficile outbreaks: A proof-of-concept study
• A holistic genome dataset of bacteria and archaea of mangrove sediments
• Reference-based variant detection with varseek
• Detection of Functional Environmental RNA (eRNA) Genes from Macro-organisms: Implications from Re-analysis of Non-laboratory Metatranscriptome Studies
• Graph-based pangenome analysis uncovers structural and functional impacts of allopolyploidization events
• Tracing the Genetic Heritage of the Kirgiz People: Dual-Wave Admixture and Ancestry-Biased Adaptation
• Germline de novo mutation rate of the highly heterozygous amphioxus genome
• Subfamily-level comparative transcriptomics of key immune regulators in plants and suspension cells reveals novel rice blast resistance genes
• Haplotype-resolved de novo assembly revealed unique characteristics of alternative lengthening of telomeres in mouse embryonic stem cells
• WeavePop: A bioinformatics workflow to explore and analyze genomic variants of eukaryotic populations
• Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot
• Genome analyses suggest recent speciation and postglacial isolation in the Norwegian lemming
• Evolutionary analysis of ascorbate-glutathione cycle genes across green plants with lineage-specific profiling in grapevine ( Vitis vinifera L.)
• A deep-time landscape of plant cis -regulatory sequence evolution
• Oxford Nanopore enhanced accuracy of long-read amplicons applied to microbial whole-genome sequencing
• Evolution and diversity of oxidoreductases involved in redox balance and energy conservation
• A Global Genomic Resource for Outcrossing Arabidopsis lyrata and Arabidopsis arenosa
• Implementation of SARS-CoV-2 genomic surveillance during the COVID-19 pandemic through an academic–public health collaboration in southeast Michigan
• Late-acting self-incompatibility in Asimina triloba: implications for the evolution of self-incompatibility in angiosperms
• Bridging the gap between legacy polymerase chain reaction-based microsatellite data with high-throughput sequencing data for conservation genomics
• AAV vector-derived elements integrate into Cas9-generated double-strand breaks and disrupt gene transcription
• Similar Genetic Routes Are Independently Targeted for Mimetic Color Convergence in Bumble Bees
• Dual-transcriptomics on microdissected cells reveals functional specialisation of symbiont-bearing-cells and contrasted responses to nutritional stress in the cereal weevil
• The genomic history of Iberian horses since the last Ice Age
• Phylogenomics, trophic ecology, and systematics of the Morchellaceae
• Genomic origins and evolution of neo-sex chromosomes in Pacific Island birds
• Dispersal and isolation of the scaly-foot snail across abyssal insular habitats and through time
• A Post‐Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA
• The reference genome for the northeastern Pacific bull kelp, Nereocystis luetkeana
• Recovering signatures of archaic hominin introgression using ancestral recombination graphs
• A haplotype-resolved, chromosome-scale genome assembly and annotation for Carya glabra (pignut hickory; Juglandaceae)
• Retrotransposon Activation in the Aged and Alzheimer’s Disease Brain Examined by Nanopore Long-read DNA Sequencing
• Genome Assembly of Gangetic Dolphin ( Platanista gangetica ) Reveals Signature of Regressive Evolution
• Evaluating the effects of archaic protein-altering variants in living human adults
• A panel of near-isogenic lines derived from locally adapted populations of a wild plant: A powerful tool for dissecting additive and non-additive effects on ecologically important traits
• Population‐level gene expression can repeatedly link genes to functions in maize
• Systematic analysis of nonsense variants uncovers peptide release rate as a novel modifier of nonsense-mediated mRNA decay
• Widespread Variation in EDNRB2 Is Associated With Diverse Melanin Loss Phenotypes Across Avian Species
• Phylogenomic Barcoding of Soil Seed Bank–Persistent and Wind‐Dispersed Non‐Native Plant Species in South Georgia
• A wild genome of the underutilized legume lablab ( Lablab purpureus ) reveals the genetic basis of domestication
• Pre-assembly NGS correction of ONT reads achieves HiFi-level assembly quality
• Scaling up orphan crop research: A global genetic perspective of cowpea ( Vigna unguiculata ) diversity from 10,617 accessions
• Tomato Brown Rugose Fruit Virus Isolate Containing A134T Amino Acid Substitution in the Movement Protein Enhanced Symptom Severity in Tomato Plants
• Beyond Structure: The Role of the Outer Integument in Embryo, Endosperm, and Seed Development in Annona
• Are genetic differences between eastern and western Golden-crowned Kinglets populations correlated with environmental variation?
• Genome sequence assembly and annotation of MATA and MATB strains of Yarrowia lipolytica
• Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data
• WITHDRAWN: ChromPhaser: A HiFi Read Phasing Framework Integrating SNPmers and Hi-C Data
• Phylogenomic challenges in polyploid-rich lineages: Insights from paralog processing and reticulation methods using the complex genus Packera (Asteraceae: Senecioneae)
• Inferring domestic goat demographic history through ancient genome imputation
• Split or spread - A spatio-temporal framework for the evolution of annual Arabis (Brassicaceae) in Eurasia
• A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures
• Challenge Specific Modulation of Responses to Adjuvant‐Induced Innate Immune Memory
• Structure and sequence evolution in the pennycress ( Thlaspi arvense ) pangenome
• Cell type-specific dysregulation of gene expression due to Chd8 haploinsufficiency during mouse cortical development
• In vitro exposure to non-antipseudomonal antibiotics (NAPA) induces Pseudomonas aeruginosa resistance to antipseudomonal antibiotics (APA)
• Integrative taxonomy of cryptic Pachypus chafers using museomics, morphometrics, barcoding, and genomic DNA analysis (Coleoptera: Scarabaeidae: Pachypodinae)
• Integrative multi-omics analysis reveals the genetic architecture of floral traits in Anthurium
• Ancient and Recent Riverine Gene Flow Contributed to the Adaptive Radiation of Sailfin Silversides in Wallace's Dreampond
• A genome assembly of the speckled dace, Rhinichthys osculus
• Host species-specific gene expression by a widespread and flexible chemosynthetic symbiont
• Late Pleistocene onset of mutualistic human/canid ( Canis spp.) relationships in subarctic Alaska
• A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii
• fCUT&Tag‐Seq: An optimized CUT&Tag‐based method for high‐resolution profiling of histone modifications and chromatin‐binding proteins in fungi
• The genome assembly of Sphaerospora molnari provides novel insights into the rapid evolution and diversification of unique lineage-specific gene groups in myxozoan parasites
• New genomic resources and the historical demography of the Tourmaline Sunangel (Trochilidae, Heliangelus exortis ) in the Colombian Andes
• A de novo genome assembly of an Angelman syndrome pig ( Sus scrofa domesticus ) model to resolve SNHG14
• Whole genome sequencing reveals variation in immune and nervous systems associated with harbor seal susceptibility to phocine distemper virus
• Pangenomics and single-cell transcriptomics uncover the genetic basis of continuous bearing trait in grapevine
• A pseudochromosomal reference genome of the golden jackal, Canis aureus
• The genome assemblies of the Tui chub, Siphateles bicolor , and Arroyo chub, Gila orcuttii
• Clonal-aggregative multicellularity tuned by salinity in a choanoflagellate
• Quantum mechanics-based multitensor AI/ML uniquely able to discover, validate, and interpret predictors from small-cohort noisy high-dimensional multiomic data
• The Genomic Basis of the Tristylous Floral Polymorphism: Evidence for a Role of Gene Duplications in a Region of Restricted Recombination
• Complex Genomic Structural Variation Underlies Climate Adaptation across Eucalyptus species
• Frequent Hybridisation Between Parapatric Lekking Bird‐of‐Paradise Species
• MosaicSim: A Novel Mosaic Variant Simulator Reveals Diminishing Returns of Ultra-High Coverage for Mosaic Variant Detection
• Haplotype-resolved diploid genome inference on pangenome graphs
• Eduomics: a Nextflow pipeline to simulate -omics data for education
• Testing for the Genomic Footprint of Conflict Between Life Stages in an Angiosperm and Moss Species
• Epithelial cell chirality emerges through the dynamic concentric pattern of actomyosin cytoskeleton
• “A genome assembly of the California flannelbush, Fremontodendron californicum ”
• De novo genome assembly, inversion detection, and worldwide adaptation on the invasive species Styela plicata
• A genome assembly of Greene’s tuctoria, Tuctoria greenei , an amphibious endemic and endangered California vernal pool grass
• A genome assembly for mule deer, Odocoileus hemionus , from Southern California
• Genome assembly of the dyeing poison frog provides insights into the dynamics of transposable element and genome-size evolution
• The Regulatory Logic of Planarian Stem Cell Differentiation
• Strain-specific structural variant landscapes shape mutation retention following mutagenesis in Caenorhabditis elegans
• A reference genome assembly for the pink volcano barnacle, Tetraclita rubescens , Nilsson-Cantell, 1931
• Unique genetic bases of repeated life-history divergence associated with high altitude adaptation in Mimulus perennials
• The genome of Hippophae salicifolia provides new insights into the sexual differentiation of sea buckthorn
• A chromosome-level genome assembly of the snow leopard, Panthera uncia
• Genomic footprints of domestication in almond ( Prunus dulcis )
• Potato dihaploids uncover diverse alleles to facilitate diploid potato breeding
• Topical Steroid Withdrawal Is a Targetable Excess of Mitochondrial NAD+
• Oncogenic roles of young human de novo genes and their potential as neoantigens in cancer immunotherapy
• Deep origins, distinct adaptations, and species-level status indicated for a glacial relict seal
• SVPG: A pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples
• The power to resolve relationships: identifying incongruence and precision of reduced representation and genome-wide data in phylogenomics and population genomics
• Base modification analysis in long read sequencing data using Minimod
• Improved Mutation Detection in Duplex Sequencing Data with Sample-Specific Error Profiles
• A chromosome-level genome assembly and resequencing data reveal low DNA methylation and reduced diversity in the solitary bee pollinator Osmia cornuta
• Evolution and functioning of an X–A balance sex-determining system in hops
• Development of a Flex-Seq SNP panel for raspberry ( Rubus idaeus L.) and validation through linkage map construction and identification of QTL for several traits of agronomic importance to raspberry breeding
• Delivering trait-enhanced varieties to African smallholders through a pangenomic breeding network
• Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)
• Long-distance gene flow and recombination shape the evolutionary history of a maize pathogen
• A transient mutational burst occurs during yeast colony development
• A draft genome assembly for the dart-poison frog Phyllobates terribilis
• Genomic Insights Into Population Structure and Demographic History of White Anglerfish ( Lophius piscatorius ) Throughout Its Range
• Cell cycle-dependent TICRR/TRESLIN and MTBP chromatin binding mechanisms and patterns
• Microbial diversity of Atlantic Rainforest ponds assessed by nanopore sequencing
• An optimised computational approach for the identification of somatic structural variants in cancer
• Homoeolog expression in polyploid wheat mutants shows limited transcriptional compensation
• Improvement of β‐Xylosidase and Endoxylanase Activities in Talaromyces amestolkiae by Genetic Manipulation of the Transcriptional Activator XlnR
• A human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability
• A near chromosome-level assembly of the serpentine endemic columbine, Aquilegia eximia
• 3D Genome Constrains Breakpoints of Inversions That Can Act as Barriers to Gene Flow in the Stickleback
• Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes
• Historical genomic variation of Eurasian otters (Lutra lutra) in Britain, from hunting trophies
• Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China
• Speciation Genomics in the Tiger Whiptail Lizards ( Aspidoscelis tigris Complex)
• From macro to micro: De novo genomes of Aedes mosquitoes enable comparative genomics among close and distant relatives

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