A Strategy for Single-Run Sequencing of the Water Buffalo Genome: (I) the Use of Third-Generation Technology to Quickly Produce Long, High-Quality Reads
Abstract
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Selection
2.2. Nucleic Acid Extraction
2.3. Library Preparation and Long-Reads Sequencing
2.4. Long-Read Data Generation
2.5. Read Preprocessing and Quality Evaluation
- porechop --i /path/to/input/directory/--o /path/to/output/file.fastq.gz--discard_middle
- NanoPlot --fastq_rich /path/to/input/file.fastq --format pdf—maxlength 200000 --outdir /path/to/output/directory
3. Results
3.1. Evaluation of Extracted DNA
3.2. Long-Read Sequencing
3.3. Read Preprocessing and Quality Evaluation
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
CNV | Copy number variant |
gDNA | Genomic DNA |
HDF5 | Hierarchical Data Format 5 |
ONT | Oxford Nanopore Technologies |
ssDNA | Single-strand DNA |
dsDNA | Double-strand DNA |
DIN | DNA Integrity Number |
WGS | Whole-genome sequencing |
TGS | Third-generation sequencing |
References
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N° | ID_Buffalo | Sex | Concentration (ng/ µL) | DIN |
---|---|---|---|---|
1 | b_1 | M | 113.7 | 9.1 |
2 | b_2 | M | 133.3 | 9.1 |
3 | b_3 | F | 156.3 | 9.3 |
4 | b_4 | M | 67.9 | 9.0 |
5 | b_5 | F | 202 | 8.8 |
Long-Reads Sequencing Details | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
N° | ID Buffalo | Uploaded Library (fmol) | Flow Cell ID | Initial Pores | Library Protocol (WGS) | Basecaller Used | Estimated Bases (Gbases) | N50 (kb) | Number of Reads (M) | Bases Called (Mbases) | |
Pass | Fail | ||||||||||
1 | b_1 | 58 | PAM72151 | 6175 | SQK-LSK110 | Guppy 6.3.9 | 135.66 | 11.27 | 15.52 | 107.99 | 21.72 |
2 | b_2 | 33 | PAM31376 | 6734 | SQK-LSK110 | Guppy 6.3.9 | 107.13 | 17.77 | 8.51 | 90.1 | 15.91 |
3 | b_3 | 32 | PAI33833 | 9177 | SQK_LSK110 | Dorado 7.1.4 | 106.64 | 12.18 | 11.78 | 65.37 | 41.64 |
4 | b_4 | 11 | PAI27564 | 5180 | SQK-LSK114 | Guppy 6.3.9 | 111.69 | 15.71 | 11.03 | 91.14 | 16.26 |
5 | b_5 | 36 | PAU60985 | 7066 | SQK-LSK114 | Dorado 7.2 | 99.35 | 15.44 | 8.84 | 66.14 | 27.45 |
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Di Maggio, F.; Nunziato, M.; Toscano, E.; Sepe, L.; Cimmino, R.; Capolongo, E.A.; Vasco, A.; Paolella, G.; Salvatore, F. A Strategy for Single-Run Sequencing of the Water Buffalo Genome: (I) the Use of Third-Generation Technology to Quickly Produce Long, High-Quality Reads. Animals 2025, 15, 2991. https://doi.org/10.3390/ani15202991
Di Maggio F, Nunziato M, Toscano E, Sepe L, Cimmino R, Capolongo EA, Vasco A, Paolella G, Salvatore F. A Strategy for Single-Run Sequencing of the Water Buffalo Genome: (I) the Use of Third-Generation Technology to Quickly Produce Long, High-Quality Reads. Animals. 2025; 15(20):2991. https://doi.org/10.3390/ani15202991
Chicago/Turabian StyleDi Maggio, Federica, Marcella Nunziato, Elvira Toscano, Leandra Sepe, Roberta Cimmino, Emanuela Antonella Capolongo, Alessandra Vasco, Giovanni Paolella, and Francesco Salvatore. 2025. "A Strategy for Single-Run Sequencing of the Water Buffalo Genome: (I) the Use of Third-Generation Technology to Quickly Produce Long, High-Quality Reads" Animals 15, no. 20: 2991. https://doi.org/10.3390/ani15202991
APA StyleDi Maggio, F., Nunziato, M., Toscano, E., Sepe, L., Cimmino, R., Capolongo, E. A., Vasco, A., Paolella, G., & Salvatore, F. (2025). A Strategy for Single-Run Sequencing of the Water Buffalo Genome: (I) the Use of Third-Generation Technology to Quickly Produce Long, High-Quality Reads. Animals, 15(20), 2991. https://doi.org/10.3390/ani15202991