GigaScience

Article	Citations
Twelve years of SAMtools and BCFtools	6415
Significantly improving the quality of genome assemblies through curation	967
SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data	735
HTSlib: C library for reading/writing high-throughput sequencing data	233
A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event	206
BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters	114
GALLO: An R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci	109
A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas	104
Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore	102
Long-read assembly of the Brassica napus reference genome Darmor-bzh	76
Comparison of long-read methods for sequencing and assembly of a plant genome	67
Inferring microbiota functions from taxonomic genes: a review	64
Parliament2: Accurate structural variant calling at scale	57
CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing	52
Chromosome-level genome assembly of the hard-shelled mussel Mytilus coruscus, a widely distributed species from the temperate areas of East Asia	49
Preventing dataset shift from breaking machine-learning biomarkers	48
Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology	48
NuCLS: A scalable crowdsourcing approach and dataset for nucleus classification and segmentation in breast cancer	44
Accelerated deciphering of the genetic architecture of agricultural economic traits in pigs using a low-coverage whole-genome sequencing strategy	44
Chromosome-level draft genome of a diploid plum (Prunus salicina)	43
BiSulfite Bolt: A bisulfite sequencing analysis platform	42
An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome	41
DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach	41
long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data	39
Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding	38

A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals	37
Understanding the impact of preprocessing pipelines on neuroimaging cortical surface analyses	36
Chromosome-level reference genome of the European wasp spiderArgiope bruennichi: a resource for studies on range expansion and evolutionary adaptation	34
The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity	33
How to remove or control confounds in predictive models, with applications to brain biomarkers	33
Genome size evolution in the diverse insect order Trichoptera	33
The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features	33
Streamlining data-intensive biology with workflow systems	31
Multi-stage malaria parasite recognition by deep learning	31
The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data	31
A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense	30
Torix Rickettsia are widespread in arthropods and reflect a neglected symbiosis	30
Fractional ridge regression: a fast, interpretable reparameterization of ridge regression	30
The germline mutational process in rhesus macaque and its implications for phylogenetic dating	29
Efficient DNA sequence compression with neural networks	29
Population modeling with machine learning can enhance measures of mental health	29
U-Limb: A multi-modal, multi-center database on arm motion control in healthy and post-stroke conditions	28
A microbial gene catalog of anaerobic digestion from full-scale biogas plants	28
Loop detection using Hi-C data with HiCExplorer	27
De novo genome assemblies of butterflies	26
Association mapping across a multitude of traits collected in diverse environments in maize	25
Localized effect of treated wastewater effluent on the resistome of an urban watershed	25
Building the mega single-cell transcriptome ocular meta-atlas	25
The rise of genomics in snake venom research: recent advances and future perspectives	24
Comparative analysis of 7 short-read sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing	24
Trajectories, bifurcations, and pseudo-time in large clinical datasets: applications to myocardial infarction and diabetes data	24
Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design	24
Label3DMaize: toolkit for 3D point cloud data annotation of maize shoots	24
SYNPRED: prediction of drug combination effects in cancer using different synergy metrics and ensemble learning	23
A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae	23
Two high-qualityde novogenomes from single ethanol-preserved specimens of tiny metazoans (Collembola)	23
Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis)	23
Chromosomal genome ofTriplophysa bleekeriprovides insights into its evolution and environmental adaptation	22
Mantis: flexible and consensus-driven genome annotation	22
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package	22
A new mass spectral library for high-coverage and reproducible analysis of the Plasmodium falciparum–infected red blood cell proteome	22
Desiderata for the development of next-generation electronic health record phenotype libraries	21
ISA API: An open platform for interoperable life science experimental metadata	21
High-throughput proteomics and in vitro functional characterization of the 26 medically most important elapids and vipers from sub-Saharan Africa	21
Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes	20
Message in a Bottle—Metabarcoding enables biodiversity comparisons across ecoregions	20
Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing	20
0s and 1s in marine molecular research: a regional HPC perspective	20
MB-GAN: Microbiome Simulation via Generative Adversarial Network	19
Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data	19
iGenomics: Comprehensive DNA sequence analysis on your Smartphone	18
M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data	18
An in vitro whole-cell electrophysiology dataset of human cortical neurons	18
Improved microbial genomes and gene catalog of the chicken gut from metagenomic sequencing of high-fidelity long reads	18
Comparative analysis of common alignment tools for single-cell RNA sequencing	18

Antibiotic resistance genes are differentially mobilized according to resistance mechanism	17
Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss	17
Efficient real-time selective genome sequencing on resource-constrained devices	17
Correcting for experiment-specific variability in expression compendia can remove underlying signals	17
Spacemake: processing and analysis of large-scale spatial transcriptomics data	16
Centering inclusivity in the design of online conferences—An OHBM–Open Science perspective	16
Agricultural plant cataloging and establishment of a data framework from UAV-based crop images by computer vision	16
What the Phage: a scalable workflow for the identification and analysis of phage sequences	16
Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods	16
DENTIST—using long reads for closing assembly gaps at high accuracy	16
Fungal and ciliate protozoa are the main rumen microbes associated with methane emissions in dairy cattle	15
AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology	15
SSNOMBACTER: A collection of scattering-type scanning near-field optical microscopy and atomic force microscopy images of bacterial cells	15
Multi-modal data collection for measuring health, behavior, and living environment of large-scale participant cohorts	15
Evolution of complex genome architecture in gymnosperms	15
Myth-busting the provider-user relationship for digital sequence information	15
A curated human cellular microRNAome based on 196 primary cell types	15
Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis	15
Benchmarking missing-values approaches for predictive models on health databases	14
Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment	14
Triku: a feature selection method based on nearest neighbors for single-cell data	14
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects	14
Genome diversity in Ukraine	14
A chromosome-level reference genome of the hazelnut, Corylus heterophylla Fisch	14
MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations	14
The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis	14
Synonymous variants that disrupt messenger RNA structure are significantly constrained in the human population	13
Identification of a differentiation stall in epithelial mesenchymal transition in histone H3–mutant diffuse midline glioma	13
Clonality, inbreeding, and hybridization in two extremotolerant black yeasts	13
BIGwas: Single-command quality control and association testing for multi-cohort and biobank-scale GWAS/PheWAS data	13
Quantifying research interests in 7,521 mammalian species with h-index: a case study	13
Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework	13
Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers	13
RNAProt: an efficient and feature-rich RNA binding protein binding site predictor	13
Open and reusable annotated mass spectrometry dataset of a chemodiverse collection of 1,600 plant extracts	13
Lilikoi V2.0: a deep learning–enabled, personalized pathway-based R package for diagnosis and prognosis predictions using metabolomics data	12
High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis	12
A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl	12
An analysis of security vulnerabilities in container images for scientific data analysis	12
Internet of Samples (iSamples): Toward an interdisciplinary cyberinfrastructure for material samples	12
Maternal plasma lipids are involved in the pathogenesis of preterm birth	12
Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater	12
Fluorescence microscopy datasets for training deep neural networks	12
Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building coralsPorites luteaandIsopora palifera	12
A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles	12
A high-throughput multiplexing and selection strategy to complete bacterial genomes	12
Chromosome-level genome assembly of the black widow spiderLatrodectus elegansilluminates composition and evolution of venom and silk proteins	12
SurvBenchmark: comprehensive benchmarking study of survival analysis methods using both omics data and clinical data	11
ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture	11
AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data	11
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources	11
ViReMa: a virus recombination mapper of next-generation sequencing data characterizes diverse recombinant viral nucleic acids	11
A proteomic approach reveals possible molecular mechanisms and roles for endosymbiotic bacteria in begomovirus transmission by whiteflies	11
DeePVP: Identification and classification of phage virion proteins using deep learning	11
High-quality genome assemblies from key Hawaiian coral species	11
Multi-dimensional leaf phenotypes reflect root system genotype in grafted grapevine over the growing season	11
A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen	11
Chromosome-level assembly and annotation of the blue catfishIctalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies	10
Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis	10
Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake	10
Monash DaCRA fPET-fMRI: A dataset for comparison of radiotracer administration for high temporal resolution functional FDG-PET	10
Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators	10
DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data	10
Tool recommender system in Galaxy using deep learning	10
Association of female reproductive tract microbiota with egg production in layer chickens	10
High-throughput microscopy reveals the impact of multifactorial environmental perturbations on colorectal cancer cell growth	10
CAT: a computational anatomy toolbox for the analysis of structural MRI data	10
Alignstein: Optimal transport for improved LC-MS retention time alignment	10
Data standardization of plant–pollinator interactions	10
Transcriptome annotation in the cloud: complexity, best practices, and cost	10
xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments	10
Best genome sequencing strategies for annotation of complex immune gene families in wildlife	10
Statistical quantification of confounding bias in machine learning models	10
Genome sequencing of deep-sea hydrothermal vent snails reveals adaptions to extreme environments	10
GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes	9
Near-chromosomalde novoassembly of Bengal tiger genome reveals genetic hallmarks of apex predation	9
Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification	9
Fully resolved assembly of Cryptosporidium parvum	9
Evaluating short-term forecasting of COVID-19 cases among different epidemiological models under a Bayesian framework	9
MBGC: Multiple Bacteria Genome Compressor	9

Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA–minus RNA sequencing data	9
Chromosome-level genome assemblies ofChanna argusandChanna maculataand comparative analysis of their temperature adaptability	9
Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnaclePollicipes pollicipes	9
Chromosome-level genome of the globe skimmer dragonfly (Pantala flavescens)	9
X-ray microtomography–based atlas of mouse cranial development	8
Genomic analyses provide insights into the evolution and salinity adaptation of halophyteTamarix chinensis	8
Making experimental data tables in the life sciences more FAIR: a pragmatic approach	8
Driftage: a multi-agent system framework for concept drift detection	8
Citation needed? Wikipedia bibliometrics during the first wave of the COVID-19 pandemic	8
Lessons learned about the biology and genomics of Diaphorina citri infection with “Candidatus Liberibacter asiaticus” by integrating new and archived organ-specific transcriptome data	8
Qiber3D—an open-source software package for the quantitative analysis of networks from 3D image stacks	8
Genomes and demographic histories of the endangeredBretschneidera sinensis(Akaniaceae)	8
Disease classification for whole-blood DNA methylation: Meta-analysis, missing values imputation, and XAI	8
GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets	8
Chromosome-level genome and the identification of sex chromosomes inUloborus diversus	8
Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim	7
File-based localization of numerical perturbations in data analysis pipelines	7
A high-quality assembled genome and its comparative analysis decode the adaptive molecular mechanism of the number one Chinese cotton variety CRI-12	7
Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix	7
Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map	7
A scalable software solution for anonymizing high-dimensional biomedical data	7
ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data	7
A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability	7
Confound-leakage: confound removal in machine learning leads to leakage	7
The complexity landscape of viral genomes	7
A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications	7
biotoolsSchema: a formalized schema for bioinformatics software description	7
An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis	7
A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)	7
Delineating regions of interest for mass spectrometry imaging by multimodally corroborated spatial segmentation	7
Genome assembly ofMusa beccariishows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes	6
The Pioneer Advantage: Filling the blank spots on the map of genome diversity in Europe	6
The founding charter of the Omic Biodiversity Observation Network (Omic BON)	6
Making Common Fund data more findable: catalyzing a data ecosystem	6
KOREF_S1: phased, parental trio-binned Korean reference genome using long reads and Hi-C sequencing methods	6
Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population	6
Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas	6
EraSOR: a software tool to eliminate inflation caused by sample overlap in polygenic score analyses	6
Chromosome-level genome assembly ofPlazaster borealissheds light on the morphogenesis of multiarmed starfish and its regenerative capacity	6
A Chromosome-level assembly of the Japanese eel genome, insights into gene duplication and chromosomal reorganization	6
Open-source benchmarking of IBD segment detection methods for biobank-scale cohorts	6
The state of Medusozoa genomics: current evidence and future challenges	6
Parvovirus dark matter in the cloaca of wild birds	6
SimFFPE and FilterFFPE: improving structural variant calling in FFPE samples	6
Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines	6
CoVEffect: interactive system for mining the effects of SARS-CoV-2 mutations and variants based on deep learning	6
Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2	6
Identifying the effect of vancomycin on health care–associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media	6
NETMAGE: A human disease phenotype map generator for the network-based visualization of phenome-wide association study results	5
learnMSA: learning and aligning large protein families	5
Interpretable network-guided epistasis detection	5
The new COST Action European Venom Network (EUVEN)—synergy and future perspectives of modern venomics	5
TheCapparis spinosavar.herbaceagenome provides the first genomic instrument for a diversity and evolution study of the Capparaceae family	5
NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data	5
Chromosome-level genome assembly of goose provides insight into the adaptation and growth of local goose breeds	5
Generation and application of pseudo–long reads for metagenome assembly	5
The Nencki-Symfonia electroencephalography/event-related potential dataset: Multiple cognitive tasks and resting-state data collected in a sample of healthy adults	5
Computational prediction of human deep intronic variation	5
Stardust: improving spatial transcriptomics data analysis through space-aware modularity optimization-based clustering	5
Bias-invariant RNA-sequencing metadata annotation	5
Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster,Mesocricetus auratus	5
A methodological approach to correlate tumor heterogeneity with drug distribution profile in mass spectrometry imaging data	5
Metaphor—A workflow for streamlined assembly and binning of metagenomes	5
Toward a scalable framework for reproducible processing of volumetric, nanoscale neuroimaging datasets	5
A novel ground truth multispectral image dataset with weight, anthocyanins, and Brix index measures of grape berries tested for its utility in machine learning pipelines	5
Fast and accurate estimation of multidimensional site frequency spectra from low-coverage high-throughput sequencing data	5
A new haplotype-resolved turkey genome to enable turkey genetics and genomics research	5
A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes	5
Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues	4
FriendlyClearMap: an optimized toolkit for mouse brain mapping and analysis	4
Publishing data to support the fight against human vector-borne diseases	4
The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics	4
Studying mutation rate evolution in primates—the effects of computational pipelines and parameter choices	4
ricu: R’s interface to intensive care data	4
A chromosome-level genome of the booklouse,Liposcelis brunnea, provides insight into louse evolution and environmental stress adaptation	4
High temporal resolution Nanopore sequencing dataset of SARS-CoV-2 and host cell RNAs	4
Honey bee (Apis mellifera) wing images: a tool for identification and conservation	4
Accurate gene consensus at low nanopore coverage	4
Computational reproducibility of Jupyter notebooks from biomedical publications	4
FAIR data station for lightweight metadata management and validation of omics studies	4
CopyDetective: Detection threshold–aware copy number variant calling in whole-exome sequencing data	4
MLcps: machine learning cumulative performance score for classification problems	4
MuLan-Methyl—multiple transformer-based language models for accurate DNA methylation prediction	4
ChemChaste: Simulating spatially inhomogeneous biochemical reaction–diffusion systems for modeling cell–environment feedbacks	4
Chromosome-level genome of the poultry shaft louse Menopon gallinae provides insight into the host-switching and adaptive evolution of parasitic lice	4
Chromosome-level genome assembly of the shuttles hoppfish, Periophthalmus modestus	4
A decade of GigaScience: A perspective on conservation genetics	4
The Global Atlas of Bamboo and Rattan (GABR) Phase II: new resources for sustainable development	4