OOIR: Observatory of International Research

Papers

(The H4-Index of GigaScience is 35. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-04-01 to 2024-04-01.)

Article	Citations
Twelve years of SAMtools and BCFtools	4587
Significantly improving the quality of genome assemblies through curation	740
SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data	557
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	183
HTSlib: C library for reading/writing high-throughput sequencing data	183
An improved pig reference genome sequence to enable pig genetics and genomics research	176
IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring	164
Construction of a chromosome-scale long-read reference genome assembly for potato	150
TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads	150
BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters	96
A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas	91
GALLO: An R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci	85
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	84
Recommendations to enhance rigor and reproducibility in biomedical research	79
High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome	74
Long-read assembly of the Brassica napus reference genome Darmor-bzh	67
Comparison of long-read methods for sequencing and assembly of a plant genome	58
Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples	58
The gene-rich genome of the scallop Pecten maximus	54
Inferring microbiota functions from taxonomic genes: a review	54
Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K)	47
Parliament2: Accurate structural variant calling at scale	47
Chromosome-level genome assembly of the hard-shelled mussel Mytilus coruscus, a widely distributed species from the temperate areas of East Asia	47
Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C	46
Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle	42

SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat	42
Genomic data imputation with variational auto-encoders	41
Chromosome-level draft genome of a diploid plum (Prunus salicina)	40
Preventing dataset shift from breaking machine-learning biomarkers	40
CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing	37
Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology	37
Multimodal signal dataset for 11 intuitive movement tasks from single upper extremity during multiple recording sessions	36
A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment	35
long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data	35
Assessment of fecal DNA extraction protocols for metagenomic studies	35