References

Batut, Bérénice, Maria Doyle, Alexandre Cormier, Anthony Bretaudeau, Laura Leroi, Erwan Corre, Stéphanie Robin, gallantries, and Cameron Hyde. “Quality Control (Galaxy Training Materials).” https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html.

ClevaLab. 2022a. “A Step-by-Step Guide to NGS.” https://www.clevalab.com/post/a-step-by-step-guide-to-ngs.

———. 2022b. “Next Generation Sequencing - a Step-by-Step Guide to DNA Sequencing.” YouTube. https://www.youtube.com/watch?v=WKAUtJQ69n8.

Hiltemann, Saskia, Helena Rasche, Simon Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel Blankenberg, Pratik D. Jagtap, et al. 2023. “Galaxy Training: A Powerful Framework for Teaching!” Edited by Francis Ouellette. PLoS Comput Biol Computational Biology 19 (1): e1010752. https://doi.org/10.1371/journal.pcbi.1010752.

Illumina. 2008. “Multiplexed Sequencing with the Illumina Genome Analyzer System.” https://www.illumina.com/documents/products/datasheets/datasheet_sequencing_multiplex.pdf.

———. 2016. “Overview of Illumina Sequencing by Synthesis Workflow.” YouTube. https://www.youtube.com/watch?v=fCd6B5HRaZ8.

———. 2017. “An Introduction to Next-Generation Sequencing Technology.” https://www.illumina.com/content/dam/illumina-marketing/documents/products/illumina_sequencing_introduction.pdf.

———. 2020. “How Short Inserts Affect Sequencing Performance.” https://support.illumina.com/ko-kr/bulletins/2020/12/how-short-inserts-affect-sequencing-performance.html.

———. 2021a. “Learn about Illumina’s Next-Generation Sequencing Workflow.” YouTube. https://www.youtube.com/watch?v=oIJaA6h2bFM.

———. 2021b. “Indexed Sequencing on Illumina Systems.” https://support-docs.illumina.com/SHARE/IndexedSeq/indexed-sequencing.pdf.

———. n.d. “Next-Generation Sequencing Glossary.” NGS Terminology. https://www.illumina.com/science/technology/next-generation-sequencing/beginners/glossary.html.

Kattenberg, Johanna Helena, Carlos Fernandez-Miñope, Norbert J. Van Dijk, Lidia Llacsahuanga Allcca, Pieter Guetens, Hugo O. Valdivia, Jean-Pierre Van Geertruyden, et al. 2023. “Malaria Molecular Surveillance in the Peruvian Amazon with a Novel Highly Multiplexed Plasmodium Falciparum AmpliSeq Assay.” Edited by Gemma Moncunill. Microbiology Spectrum 11 (2): e00960–22. https://doi.org/10.1128/spectrum.00960-22.

Kattenberg, Johanna Helena, Hong Van Nguyen, Hieu Luong Nguyen, Erin Sauve, Ngoc Thi Hong Nguyen, Ana Chopo-Pizarro, Hidayat Trimarsanto, et al. 2022. “Novel Highly-Multiplexed AmpliSeq Targeted Assay for Plasmodium Vivax Genetic Surveillance Use Cases at Multiple Geographical Scales.” Frontiers in Cellular and Infection Microbiology 12 (August): 953187. https://doi.org/10.3389/fcimb.2022.953187.

Launen, Loren. 2017. “Illumina Sequencing (for Dummies).” https://kscbioinformatics.wordpress.com/2017/02/13/illumina-sequencing-for-dummies-samples-are-sequenced/.

Ledergerber, C., and C. Dessimoz. 2011. “Base-Calling for Next-Generation Sequencing Platforms.” Briefings in Bioinformatics 12 (5): 489–97. https://doi.org/10.1093/bib/bbq077.

MalariaGEN, Muzamil Mahdi Abdel Hamid, Mohamed Hassan Abdelraheem, Desmond Omane Acheampong, Ambroise Ahouidi, Mozam Ali, Jacob Almagro-Garcia, et al. 2023. “Pf7: An Open Dataset of Plasmodium Falciparum Genome Variation in 20,000 Worldwide Samples.” Wellcome Open Research 8 (January): 22. https://doi.org/10.12688/wellcomeopenres.18681.1.

Piper, Mary E., Meeta Mistry, Jihe Liu, William J. Gammerdinger, and Radhika S. Khetani. 2022. “Hbctraining/Intro-to-Rnaseq-Hpc-Salmon-Flipped: Introduction to RNA-Seq Using Salmon Lessons from HCBC (First Release),” January. https://doi.org/10.5281/ZENODO.5833880.

Rausch, Tobias. 2022. “Methods in Genomic Variant Calling.” EMBL-EBI. https://doi.org/10.6019/TOL.GenomicVariantCalling-w.2022.00001.1 .

Rochette, Nicolas C., Angel G. Rivera‐Colón, Jessica Walsh, Thomas J. Sanger, Shane C. Campbell‐Staton, and Julian M. Catchen. 2023. “On the Causes, Consequences, and Avoidance of <Span Style="font-Variant:small-Caps;">PCR</Span> Duplicates: Towards a Theory of Library Complexity.” Molecular Ecology Resources 23 (6): 1299–1318. https://doi.org/10.1111/1755-0998.13800.

Rodriguez, Raphaël, and Yamuna Krishnan. 2023. “The Chemistry of Next-Generation Sequencing.” Nature Biotechnology 41 (12): 1709–15. https://doi.org/10.1038/s41587-023-01986-3.

Shendure, Jay, Shankar Balasubramanian, George M. Church, Walter Gilbert, Jane Rogers, Jeffery A. Schloss, and Robert H. Waterston. 2017. “DNA Sequencing at 40: Past, Present and Future.” Nature 550 (7676): 345–53. https://doi.org/10.1038/nature24286.

University of Exeter DNA sequencing service. “Introduction to Genomics.” https://biomedicalhub.github.io/genomics/01-part1-introduction.html.

Wolff, Joachim, Bérénice Batut, and Helena Rasche. “Mapping (Galaxy Training Materials).” https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/tutorial.html.