| # | Title | Journal | Year | Citations |
|---|
| 1 | Second-generation PLINK: rising to the challenge of larger and richer datasets | GigaScience | 2015 | 8,062 |
| 2 | Twelve years of SAMtools and BCFtools | GigaScience | 2021 | 4,546 |
| 3 | SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler | GigaScience | 2012 | 4,510 |
| 4 | SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data | GigaScience | 2018 | 1,265 |
| 5 | Taxonomic structure and functional association of foxtail millet root microbiome | GigaScience | 2017 | 1,228 |
| 6 | EMPeror: a tool for visualizing high-throughput microbial community data | GigaScience | 2013 | 1,096 |
| 7 | PRSice-2: Polygenic Risk Score software for biobank-scale data | GigaScience | 2019 | 940 |
| 8 | The need to approximate the use-case in clinical machine learning | GigaScience | 2017 | 911 |
| 9 | Significantly improving the quality of genome assemblies through curation | GigaScience | 2021 | 739 |
| 10 | The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome | GigaScience | 2012 | 671 |
| 11 | Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes | GigaScience | 2017 | 602 |
| 12 | Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species | GigaScience | 2013 | 582 |
| 13 | Data access for the 1,000 Plants (1KP) project | GigaScience | 2014 | 582 |
| 14 | SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data | GigaScience | 2020 | 578 |
| 15 | The intriguing evolution of effect sizes in biomedical research over time: smaller but more often statistically significant | GigaScience | 2018 | 531 |
| 16 | The 3,000 rice genomes project | GigaScience | 2014 | 451 |
| 17 | Clustering trees: a visualization for evaluating clusterings at multiple resolutions | GigaScience | 2018 | 447 |
| 18 | rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data | GigaScience | 2019 | 428 |
| 19 | Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads | GigaScience | 2015 | 381 |
| 20 | De novo assembly of the cattle reference genome with single-molecule sequencing | GigaScience | 2020 | 380 |
| 21 | The 3,000 rice genomes project: new opportunities and challenges for future rice research | GigaScience | 2014 | 337 |
| 22 | The role of reporting standards for metabolite annotation and identification in metabolomic studies | GigaScience | 2013 | 333 |
| 23 | BLINK: a package for the next level of genome-wide association studies with both individuals and markers in the millions | GigaScience | 2019 | 314 |
| 24 | zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs | GigaScience | 2018 | 265 |
| 25 | EEG dataset and OpenBMI toolbox for three BCI paradigms: an investigation into BCI illiteracy | GigaScience | 2019 | 243 |
| 26 | SmileFinder: a resampling-based approach to evaluate signatures of selection from genome-wide sets of matching allele frequency data in two or more diploid populations | GigaScience | 2015 | 241 |
| 27 | Draft genome of the living fossil Ginkgo biloba | GigaScience | 2016 | 232 |
| 28 | Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification | GigaScience | 2013 | 227 |
| 29 | Advanced lesion symptom mapping analyses and implementation as BCBtoolkit | GigaScience | 2018 | 226 |
| 30 | The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum | GigaScience | 2017 | 224 |
| 31 | 1399 H&E-stained sentinel lymph node sections of breast cancer patients: the CAMELYON dataset | GigaScience | 2018 | 221 |
| 32 | A reference human genome dataset of the BGISEQ-500 sequencer | GigaScience | 2017 | 219 |
| 33 | Deep machine learning provides state-of-the-art performance in image-based plant phenotyping | GigaScience | 2017 | 216 |
| 34 | NCBI BLAST+ integrated into Galaxy | GigaScience | 2015 | 213 |
| 35 | Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity | GigaScience | 2018 | 209 |
| 36 | Ultra-deep, long-read nanopore sequencing of mock microbial community standards | GigaScience | 2019 | 209 |
| 37 | A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer | GigaScience | 2014 | 208 |
| 38 | Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database | GigaScience | 2016 | 204 |
| 39 | Connections between the human gut microbiome and gestational diabetes mellitus | GigaScience | 2017 | 204 |
| 40 | Genome sequence of the olive tree, Olea europaea | GigaScience | 2016 | 201 |
| 41 | LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads | GigaScience | 2015 | 196 |
| 42 | The sponge microbiome project | GigaScience | 2017 | 193 |
| 43 | Construction of the third-generation Zea mays haplotype map | GigaScience | 2018 | 191 |
| 44 | HTSlib: C library for reading/writing high-throughput sequencing data | GigaScience | 2021 | 191 |
| 45 | A field guide for the compositional analysis of any-omics data | GigaScience | 2019 | 187 |
| 46 | An improved pig reference genome sequence to enable pig genetics and genomics research | GigaScience | 2020 | 187 |
| 47 | 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 | GigaScience | 2021 | 187 |
| 48 | The ocean sampling day consortium | GigaScience | 2015 | 185 |
| 49 | EEG datasets for motor imagery brain–computer interface | GigaScience | 2017 | 180 |
| 50 | Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer | GigaScience | 2016 | 176 |
