Genotype and SNP calling from next-generation sequencing data

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556

A framework for variation discovery and genotyping using next-generation DNA sequencing data

DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,457

Velvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint

Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,575

A map of human genome variation from population-scale sequencing.

The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877

dbSNP: the NCBI database of genetic variation

Sherry, S. T. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.308 · Cited by 7,502

Sequencing technologies – the next generation

Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066

Genetic data support reproductively isolated species in the endemic Cladophoraceae (Chlorophyta) of Lake Baikal, Russia

Martínez, S. D., Boedeker, C., & Zuccarello, G. C. (2020) · Phycologia · doi:10.1080/00318884.2020.1775461 · Cited by 5

OMICS PLATFORM TECHNOLOGIES FOR DISCOVERY AND UNDERSTANDING THE SYSTEMS BIOLOGY OF OIL PALM

Ramli, U. S. (2020) · Journal of Oil Palm Research · doi:10.21894/jopr.2020.0084 · Cited by 5

Species identification in Haliotis genus from the northeastern Pacific Ocean using genome-wide RAD-SNPs

Vargas‐Peralta, C. E., Araneda, C., Galindo‐Sánchez, C. E., Larraín, M. A., del Río-Portilla, M. Á., & la Cruz, F. L. (2022) · Food Control · doi:10.1016/j.foodcont.2022.108979 · Cited by 5

A new resource of single nucleotide polymorphisms in the Japanese eel Anguilla japonica derived from restriction site-associated DNA

Sekino, M., Nakamichi, R., Iwasaki, Y., Tanabe, A. S., Fujiwara, A., Yasuike, M., Shiraishi, M., & Saitoh, K. (2016) · Ichthyological Research · doi:10.1007/s10228-016-0518-7 · Cited by 5

Value of Mendelian Laws of Segregation in Families: Data Quality Control, Imputation, and Beyond

Blue, E., Sun, L., Tintle, N., & Wijsman, E. M. (2014) · Genetic Epidemiology · doi:10.1002/gepi.21821 · Cited by 5

Computational Methods Used in Systems Biology

Balik-Meisner, M. R., & Reif, D. M. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-801564-3.00005-5 · Cited by 5

Bootstrap aggregating of classification and regression trees in identification of single nucleotide polymorphisms

Hasibuan, L. S., Hudachair, N., & Istiadi, M. A. (2017) · International Conference on Advanced Computer Science and Information Systems · doi:10.1109/icacsis.2017.8355068 · Cited by 5

The ability of ddRAD-Seq to estimate genetic diversity and genetic introgression in endangered native livestockPreprint

Tezuka, A., Takasu, M., Tozaki, T., & Nagano, A. J. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/454108 · Cited by 5

Inherent population structure determines the importance of filtering parameters for reduced representation sequencing analysesPreprint

Selechnik, D., Richardson, M. F., Hess, M. K., Hess, A. S., Dodds, K. G., Martin, M. V., Chan, T. C., Cardilini, A. P. A., Sherman, C. D. H., Shine, R., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.14.383240 · Cited by 5

Distinct sequencing success at non-B-DNA motifsPreprint

Weissensteiner, M. H., Cremona, M. A., Guiblet, W. M., Stoler, N., Harris, R. S., Čechová, M., Eckert, K. A., Chiaromonte, F., Huang, Y.-F., & Makova, K. D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.13.495922 · Cited by 5

FrAnTK: a Frequency-based Analysis ToolKit for efficient exploration of allele sharing patterns in present-day and ancient genomic datasets

Moreno-Mayar, J. V. (2022) · G3 Genes|Genomes|Genetics · doi:10.1093/g3journal/jkab357 · Cited by 4

Can We Convert Genotype Sequences Into Images for Cases/Controls Classification?

Muneeb, M., Feng, S. F., & Henschel, A. (2022) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2022.914435 · Cited by 4

Genome-wide copy number variation regions in indigenous (Bos indicus) cattle breeds of Tamil Nadu, India

Vani, S., Balasubramanyam, D., Tirumurugaan, K. G., Gopinathan, A., & Karthickeyan, S. M. K. (2024) · Animal Bioscience · doi:10.5713/ab.23.0525 · Cited by 4

Comprehensive insights on association mapping in perennial fruit crops breeding – Its implications, current status and future perspectives

Zadokar, A., Sharma, P., & Sharma, R. (2024) · Plant Science · doi:10.1016/j.plantsci.2024.112281 · Cited by 4

Contribution of Range‐Wide and Short‐Scale Chemical Soil Variation to Local Adaptation in a Tropical Montane Forest Tree

Arenas, S., Cruz‐Nicolás, J., Giles‐Pérez, G., Barrera‐Redondo, J., Reyes‐Galindo, V., Mastretta‐Yanes, A., Aguirre‐Planter, E., Eguiarte, L. E., & Jaramillo‐Correa, J. P. (2025) · Evolutionary Applications · doi:10.1111/eva.70116 · Cited by 4

Smart-SNPer: Automated crRNA design for ultrasensitive RPA-Cas12a SNP detection

Han, L., Feng, W., Wang, L., Chen, F., Tan, T., Zhu, Y., Li, W., Yang, Y., Xu, W., Li, Y., et al. (2025) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2025.117909 · Cited by 4

A Whole-Genome Sequencing-Based SNP Protocol for Accurate Plant Variety Identification: Application in Blueberry

Furtado, A., Gunther, T., & Henry, R. J. (2025) · Applied Biosciences · doi:10.3390/applbiosci4040051 · Cited by 4

Genomic consequences of residual recombination in a hybrid apomictic hickory complex

Zhang, W.-P., Glémin, S., Pang, X., Kang, M., Zhang, D., Lascoux, M., & Bai, W. (2026) · Nature Communications · doi:10.1038/s41467-026-68867-6 · Cited by 4

Simulation-guided DNAzyme based nanomachine design for identifying single nucleotide variants

Zhang, L., Zhang, Z., Ou, X., Wang, Y., Yang, L., Weng, Z., & Xie, G. (2020) · Sensors and Actuators B Chemical · doi:10.1016/j.snb.2020.128719 · Cited by 4

A novel nonlinear dimension reduction approach to infer population structure for low-coverage sequencing data

Zhang, M., Liu, Y., Zhou, H., Watkins, J. C., & Zhou, J. J. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04265-7 · Cited by 4

Analysis of the Batch Effect Due to Sequencing Center in Population Statistics Quantifying Rare Events in the 1000 Genomes Project

Maceda, I., & Lao, Ó. (2021) · Genes · doi:10.3390/genes13010044 · Cited by 4

Method for Identifying Sequence Motifs in Pre-miRNAs for Small-Molecule Binding

Takashima, Y., Murata, A., Iida, K., Sugai, A., Hagiwara, M., & Nakatani, K. (2022) · ACS Chemical Biology · doi:10.1021/acschembio.2c00452 · Cited by 4

Assessing the population genetic structure of introduced rainbow trout (Oncorhynchus mykiss) in the Lake Tahoe basin: implications for hybridization potential during the reintroduction of native Lahontan cutthroat trout (O. clarkii henshawi)

Galland, L. M., Parchman, T. L., & Peacock, M. M. (2024) · Hydrobiologia · doi:10.1007/s10750-023-05426-w · Cited by 4

Generative haplotype prediction outperforms statistical methods for small variant detection in next-generation sequencing data

O’Fallon, B. D., Bolia, A., Durtschi, J., Yang, L., Fredrickson, E. D., Noble, K., COLEMAN, J., & Best, H. D. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae565 · Cited by 4

Emerging Approaches Based on Genome-Wide Association Studies (GWAS) for Crop Disease Tolerance

Dubey, S., & Mohanan, A. (2024) · Interdisciplinary biotechnological advances · doi:10.1007/978-981-97-7510-1_5 · Cited by 5

vcfgl: a flexible genotype likelihood simulator for VCF/BCF files

Altinkaya, I., Nielsen, R., & Korneliussen, T. S. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf098 · Cited by 4

Signatures of selective sweeps in urban and rural white clover populations

Santangelo, J. S., Johnson, M. T. J., & Ness, R. W. (2025) · Evolution · doi:10.1093/evolut/qpaf138 · Cited by 4

Likelihood-based complex trait association testing for arbitrary depth sequencing data

Yan, S., Yuan, S., Xu, Z. Q., Zhang, B., Zhang, B., Kang, G., Byrnes, A., & Li, Y. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv307 · Cited by 4

Efficiently Storing and Analyzing Genome Data in Database Systems

Dorok, S., Breß, S., Teubner, J., Läpple, H., Saake, G., & Markl, V. (2017) · Datenbank-Spektrum · doi:10.1007/s13222-017-0254-9 · Cited by 4

Genetic Diversity of Northern Wheatgrass (Elymus lanceolatus ssp. lanceolatus) as Revealed by Genotyping-by-Sequencing

Li, P., Bhattarai, S., Peterson, G., Coulman, B. E., Schellenberg, M. P., Biligetu, B., & Fu, Y. (2018) · Diversity · doi:10.3390/d10020023 · Cited by 4

Integrative omics – An arsenal for drug discovery

Singh, R. S., Angra, V., Singh, A. K., Masih, G. D., & Medhi, B. (2022) · Indian Journal of Pharmacology · doi:10.4103/ijp.ijp_53_22 · Cited by 4

NGS allele counts versus called genotypes for testing genetic association

Silos, R. G., Fischer, C., & Bermejo, J. L. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.07.016 · Cited by 4

Whole genome re-sequencing : lessons from unmapped reads

Gouin, A., Nouhaud, P., Legeai, F., Rizk, G., Simon, J., & Lemaitre, C. (2013) · HAL · Cited by 4

TarSeqQC: Quality control on targeted sequencing experiments in R

Merino, G. A., Murua, Y. A., Fresno, C., Sendoya, J. M., Golubicki, M., Iseas, S., Coraglio, M. F., Podhajcer, O. L., Llera, A. S., & Fernández, E. A. (2017) · Human Mutation · doi:10.1002/humu.23204 · Cited by 4

Detecting sequence variants in clinically important protozoan parasites

Calarco, L., Barratt, J., & Ellis, J. (2019) · International Journal for Parasitology · doi:10.1016/j.ijpara.2019.10.004 · Cited by 4

Gehört die statistische Signifikanz aufs Altenteil?

Richter, A., & Zink, A. (2020) · Zeitschrift für Rheumatologie · doi:10.1007/s00393-020-00835-x · Cited by 4

CAPG: comprehensive allopolyploid genotyper

Kulkarni, R., Zhang, Y., Cannon, S. B., & Dorman, K. S. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac729 · Cited by 4

DiSNPindel: improved intra-individual SNP and InDel detection in direct amplicon sequencing of a diploid

Deng, J., Huang, H., Yu, X., Jin, J. D., Lin, W., Li, F., Song, Z., Li, M., & Gan, S. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0790-y · Cited by 4

Application of decision tree classifier for single nucleotide polymorphism discovery from next-generation sequencing data

Istiadi, M. A., Kusuma, W. A., & Tasma, I. M. (2014) · International Conference on Advanced Computer Science and Information Systems · doi:10.1109/icacsis.2014.7065832 · Cited by 4

Comparison of three summary statistics for ranking genes in genome-wide association studies

Freytag, S., & Bickeböller, H. (2013) · Statistics in Medicine · doi:10.1002/sim.6063 · Cited by 4

An Introduction to Personalized Medicine

Stone, A., & Bornhorst, J. A. (2012) · Elsevier eBooks · doi:10.1016/b978-0-12-385467-4.00006-3 · Cited by 4

Development of single‐copy nuclear intron markers for species‐level phylogenetics: Case study with Paullinieae (Sapindaceae)1

Onyenedum, J. G., Sass, C., & Specht, C. D. (2017) · Applications in Plant Sciences · doi:10.3732/apps.1700051 · Cited by 4

A graph based model for multiple biological data sources integration

Hanafi, H., Rafii, F., Hassani, B. D. R., & Kbir, M. A. (2018) · International Conference on Smart City Applications (SCA) · doi:10.1145/3286606.3286826 · Cited by 4

PyVar: An Extensible Framework for Variant Annotator ComparisonPreprint

Wertz, J., Liao, Q., Bair, T., & Chimenti, M. S. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/078386 · Cited by 4

Human genetics and clinical aspects of neurodevelopmental disordersPreprint

Lyon, G. J., & O'Rawe, J. (2013) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/000687 · Cited by 6

Single Nucleotide Polymorphism Typing

Srinivasan, S., & Batra, J. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20127-1 · Cited by 4

Testing pipelines for genome-wide SNP calling from Genotyping-By-Sequencing (GBS) data for Pinus ponderosaPreprint

Shu, M., & Moran, E. (2020) · doi:10.21203/rs.3.rs-32336/v1 · Cited by 4

Analytical Pipelines for the GBS Analysis

Rachappanavar, V., Padiyal, A., Sharma, J. K., & Negi, N. (2022) · Wiley eBooks · doi:10.1002/9781119745686.ch8 · Cited by 4

Population structure of Puccinia striiformis f. sp. tritici, the cause of wheat stripe rust, in western Canada

Brar, G. S. (2015) · University Library - University of Saskatchewan (University of Saskatchewan) · Cited by 4

Ancient DNA sheds light on the funerary practices of late Neolithic collective burial in southern France

Arzelier, A., Belvalet, H. D., Pemonge, M., Garberi, P., Binder, D., Duday, H., Deguilloux, M., & Pruvost, M. (2024) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2024.1215 · Cited by 3

Genotyping Error Detection and Customised Filtration for SNP Datasets

Kan‐Lingwood, N. Y., Sagi, L., Mazie, S., Shahar, N., Bitton, L. Z., Templeton, A. R., Rubenstein, D. I., Bouskila, A., & Bar‐David, S. (2024) · Molecular Ecology Resources · doi:10.1111/1755-0998.14033 · Cited by 3

Simulating Genetic Mixing in Strongly Structured Populations of the Threatened Southern Brown Bandicoot (Isoodon obesulus)

Black, J. G., Cooper, S. J., Schmidt, T. L., & Weeks, A. R. (2024) · Evolutionary Applications · doi:10.1111/eva.70050 · Cited by 3

PopGLen—a Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods

Nolen, Z. J. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf105 · Cited by 3

Applying weighted Cox regression to genome-wide association studies of time-to-event phenotypes

Li, Y., Ma, Y., He, X., Sun, Y., Zhu, M., Yue, W., Zhou, W., & Bi, W. (2025) · Nature Computational Science · doi:10.1038/s43588-025-00864-z · Cited by 3

Benchmarking imputation accuracy in the presence or absence of a reference panel

Topaloudis, A., Cumer, T., Lavanchy, E., Hewett, A. M., Salvy, M. B., Ducrest, A., Simon, C., Almasi, B., Roulin, A., Delaneau, O., et al. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag094 · Cited by 3

The genetic landscape of human functional brain connectivity

Maciel, B. D. A. P. C., Schipper, M., Romero, C., de Leeuw, C., Helwegen, K., Posthuma, D., Savage, J. E., & van den Heuvel, M. P. (2026) · Nature Communications · doi:10.1038/s41467-026-69442-9 · Cited by 3

Temporal dynamics of color polymorphism and hybridization in Colias butterflies

Jahner, J. P., Forister, M. L., Parchman, T. L., Burdo, S. M., McFarlane, S. E., Buerkle, C. A., Nice, C. C., Fordyce, J. A., & Shapiro, A. M. (2026) · Evolution · doi:10.1093/evolut/qpag064 · Cited by 3

A Guide to Phylogenomic Inference

Patané, J. S. L., Martins, J., & Setúbal, J. C. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-3838-5_11 · Cited by 3

On forensic likelihood ratios from low-coverage sequencing

Ouerghi, F., Krane, D. E., & Edge, M. D. (2024) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2025.103302 · Cited by 3

Advancing ornamental plant breeding through genomic technologies: opportunities, challenges, and future directions

K., M., Pagariya, M. C., Jadhav, P. R., Gawade, N. S., Sarode, D. K., Karkute, S. G., Kardile, H. B., Deshmukh, R. K., Suprasanna, P., & Kawar, P. G. (2025) · Functional & Integrative Genomics · doi:10.1007/s10142-025-01640-y · Cited by 3

Development of an Economic-trait Genetic Marker by Applying Next-generation Sequencing Technologies in a Whole Genome

Gim, J., & Kim, H. (2014) · Journal of Life Science · doi:10.5352/jls.2014.24.11.1258 · Cited by 3

Synthesis of a fluorescence resonance energy transfer-based probe containing a tricyclic nucleoside analog for single nucleotide polymorphism typing

Hayai, A., Maeda, Y., & Ueno, Y. (2016) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2016.06.024 · Cited by 3

Clinical Genome Sequencing

Hambuch, T. M., Mayfield, J. E., Ajay, S., Hogue, M., Mead, C.-L., & Ramos, E. (2014) · Elsevier eBooks · doi:10.1016/b978-0-12-404748-8.00002-2 · Cited by 3

GGTyper: genotyping complex structural variants using short-read sequencing data

Mirus, T., Lohmayer, R., Döhring, C., Halldórsson, B. V., & Kehr, B. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae391 · Cited by 4

Natural Selection Associated With Infectious Diseases

Fumagalli, M., & Balloux, F. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-420190-3.00011-9 · Cited by 3

In silico approaches to identify the functional and structural effects of non-synonymous SNPs in selective sweeps of the Berkshire pig genome

Shin, D., Oh, J.-D., Won, K.-H., & Song, K. (2018) · Asian-Australasian Journal of Animal Sciences · doi:10.5713/ajas.17.0211 · Cited by 3

The sequencing and interpretation of the genome obtained from a Serbian individual

Ismail, W. M., Pagel, K. A., Pejaver, V. R., Zhang, S. V., Casasa, S., Mort, M. E., Cooper, D. N., Hahn, M. W., & Predrag Radivojac, A. (2018) · PLoS ONE · doi:10.1371/journal.pone.0208901 · Cited by 3

SNP hot-spots in the clam parasite QPX

Bassim, S., & Allam, B. (2018) · BMC Genomics · doi:10.1186/s12864-018-4866-8 · Cited by 4

Epigenome-Wide DNA Methylation Profiles in Oral Cancer

Chatterjee, R., Das, S., Chandra, A., & Basu, B. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-814513-5.00014-3 · Cited by 3

DETERMINATION OF MALIGNANT MELANOMA BY ANALYSIS OF VARIATION VALUES

ESİM, A. K., Kaya, H., & Alcan, V. (2019) · Turkish Journal of Engineering · doi:10.31127/tuje.472328 · Cited by 3

Mapping of the chicken cleft primary palate mutation on chromosome 11 and sequencing of the 4.9 Mb linked region

Youngworth, I., & Delany, M. E. (2020) · Animal Genetics · doi:10.1111/age.12927 · Cited by 3

Next Generation Sequencing

Hambuch, T. M., & Mayfield, J. (2014) · Elsevier eBooks · doi:10.1016/b978-0-12-386456-7.07717-0 · Cited by 3

ESREEM: Efficient Short Reads Error Estimation Computational Model for Next-generation Genome Sequencing

Tahir, M., Sardaraz, M., Mehmood, Z., & Khan, M. S. (2020) · Current Bioinformatics · doi:10.2174/1574893615999200614171832 · Cited by 3

High-Throughput Genotyping Technologies in Plant Taxonomy

Danilevicz, M. F., Fernandez, C. G. T., Marsh, J. I., Bayer, P. E., & Edwards, D. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0997-2_9 · Cited by 3

Correcting Bias in Allele Frequency Estimates Due to an Observation Threshold: A Markov Chain Analysis

Gossmann, T. I., & Waxman, D. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac047 · Cited by 3

vcferr: Development, validation, and application of a single nucleotide polymorphism genotyping error simulation framework

Nagraj, V., Scholz, M. B., Jessa, S., Ge, J., Woerner, A. E., Huang, M., Budowle, B., & Turner, S. (2022) · F1000Research · doi:10.12688/f1000research.122840.1 · Cited by 3

Genetic changes in F1 hybrids of the genetically divergent Solanum L., Solanum melongena L. × Solanum aethiopicum L.

Ning, Y., Gan, G., Li, D., Li, W., Jiang, Y., Yang, Q., Wang, P., Li, W., & Wang, Y. (2022) · Plant Growth Regulation · doi:10.1007/s10725-022-00926-6 · Cited by 3

Cytokine gene polymorphism and parasite susceptibility in free-living rodents: Importance of non-coding variants

Kloch, A., Mierzejewska, E. J., Welc-Falęciak, R., Bajer, A., & Biedrzycka, A. (2023) · PLoS ONE · doi:10.1371/journal.pone.0258009 · Cited by 3

Genomics Assisted Breeding Strategy in Flax

Khan, N., Shazadee, H., Cloutier, S., & You, F. M. (2023) · Compendium of plant genomes · doi:10.1007/978-3-031-16061-5_12 · Cited by 3

Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle

da Silva, J. M., Giachetto, P. F., da Silva, L. O. C., Cintra, L. C., Paiva, S. R., Caetano, A. R., & Yamagishi, M. E. B. (2015) · PLoS ONE · doi:10.1371/journal.pone.0136035 · Cited by 5

A novel framework for analyzing somatic copy number aberrations and tumor subclones for paired heterogeneous tumor samples

Xia, H., Li, A., Yu, Z., Liu, X., & Feng, H. (2015) · Bio-Medical Materials and Engineering · doi:10.3233/bme-151487 · Cited by 3

Haploid to diploid alignment for variation calling assessment

Mäkinen, V., & Rahkola, J. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-s15-s13 · Cited by 3

Variant genotyping with gap filling

Walve, R., Salmela, L., & Mäkinen, V. (2017) · PLoS ONE · doi:10.1371/journal.pone.0184608 · Cited by 3

Computational Tools for Population Genomics

Salojärvi, J. (2018) · Population genomics · doi:10.1007/13836_2018_57 · Cited by 3

Identification of key genes related to seedlessness by genome-wide detection of structural variation and transcriptome analysis in ‘Shijiwuhe’ pear

Liu, Y., Sun, J., Zhang, M., Yang, G., Wang, R., Xu, J., Li, Q., Zhang, S., Wen-quan, L., Hao, B., et al. (2020) · Gene · doi:10.1016/j.gene.2020.144480 · Cited by 3

Genotyping of Single Nucleotide Polymorphisms

Tian, Y., Ran, T., & Gao, Z. (2015) · RNA technologies · doi:10.1007/978-3-319-17305-4_6 · Cited by 3

Genomics Approaches to Mining Barley Germplasm Collections

Mascher, M., Sato, K., & Steffenson, B. J. (2018) · Compendium of plant genomes · doi:10.1007/978-3-319-92528-8_11 · Cited by 3

Sampling Variation of RAD-Seq Data from Diploid and Tetraploid Potato (Solanum tuberosum L.)

Dang, Z., Yang, J., Wang, L., Tao, Q., Zhang, F., Zhang, Y., & Luo, Z. (2021) · Plants · doi:10.3390/plants10020319 · Cited by 3

DNA, RNA Chemical Properties (Including Sequencing and Next-Generation Sequencing)

Datto, M. B., & Lundblad, R. L. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-394447-4.10006-9 · Cited by 3

SNP Array Development, Genotyping, Data Analysis, and Applications

Liu, S., Zeng, Q., Wang, X., & Liu, Z. (2017) · Wiley eBooks · doi:10.1002/9781118782392.ch18 · Cited by 3

An empirical evaluation of genotype imputation of ancient DNAPreprint

Ausmees, K., Sánchez‐Quinto, F., Jakobsson, M., & Nettelblad, C. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.22.473913 · Cited by 3

Whole Genome Sequencing-based Characterization of Human Genome Variation and Mutation Burden in BotswanaPreprint

Thami, P. K., Choga, W. T., Mulisa, D. D., Dandara, C., Shevchenko, A. K., Leteane, M. M., Novitsky, V., O’Brien, S. J., Essex, M., Gaseitsiwe, S., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.15.422821 · Cited by 3

Advances and Applicability of Genotyping Technologies in Cotton Improvement

Bhardwaj, S., Devkar, V., Kumar, A., Alisha, A., Sharma, S., Deshmukh, R. K., & Patil, G. (2022) · Wiley eBooks · doi:10.1002/9781119745686.ch11 · Cited by 3

Inferring drift, genetic differentiation, and admixture graphs from low-depth sequencing dataPreprint

Rasmussen, M. S., Wiuf, C., & Albrechtsen, A. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.29.577762 · Cited by 3

DeepBioSim: Efficient and Versatile Methods for Microbiome Data Simulation with Minimal Statistical AssumptionsPreprint

Shen, Y., Rajaram, S. V., Wang, W., & Zeng, E. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.21.670443 · Cited by 3

High‐throughput genotyping in estimating genetic resources and detecting pathogens in aquaculture

Li, C., & Jiang, J. (2023) · Journal of the World Aquaculture Society · doi:10.1111/jwas.12996 · Cited by 2

Analysis of genotypes and biochemical phenotypes of neonates with abnormal metabolism of butyrylcarnitine

Wu, D., Yang, R., Fang, K., Chen, L. I. U., Tang, J., Yu, M., & Zhao, Z. (2023) · Journal of Zhejiang University (Medical Sciences) · doi:10.3724/zdxbyxb-2023-0459 · Cited by 2

Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking

Sergi, A., Beltrame, L., Marchini, S., & Masseroli, M. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05793-8 · Cited by 2

Antimalarial mechanism of action of the natural product 9-methoxystrobilurin G

Shaw, P. J., Prommana, P., Thongpanchang, C., Kamchonwongpaisan, S., Kongkasuriyachai, D., Wang, Y., Zhou, Z., & Zhou, Y. (2024) · Molecular Omics · doi:10.1039/d4mo00088a · Cited by 2

Next-Generation Sequencing and Genomic Data Analysis

Kumar, V., Gangani, S., Shukla, R., Prajapati, S. K., Shekhar, H., & Shukla, V. (2024) · Springer eBooks · doi:10.1007/978-981-97-7123-3_3 · Cited by 2

Variant Calling Using NGS Data in European Aspen (Populus tremula)

Wang, J., Scofield, D. G., Street, N. R., & Ingvarsson, P. K. (2015) · Springer eBooks · doi:10.1007/978-3-319-17157-9_4 · Cited by 6

ngsTools: methods for population genetics analyses from next-generation sequencing data

Fumagalli, M., Vieira, F. G., Linderoth, T. P., & Nielsen, R. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu041 · Cited by 252

Coverage recommendation for genotyping analysis of highly heterologous species using next-generation sequencing technology

Song, K., Li, L., & Zhang, G. (2016) · Scientific Reports · doi:10.1038/srep35736 · Cited by 82

An integrated approach for SNP calling based on population of genomes

Vo, N. S., Tran, Q., & Phan, V. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-s10-p30

LD-based SNP and genotype calling from next-generation sequencing reads.

Menelaou, A. (2012) · Oxford University Research Archive (ORA) (University of Oxford) · doi:10.5287/ora-z5x684ymn