OOIR: Observatory of International Research

Papers

(The H4-Index of GigaScience is 32. 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 2020-11-01 to 2024-11-01.)

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
Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology	48
Preventing dataset shift from breaking machine-learning biomarkers	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
DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach	41
An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome	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 haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features	33
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