FAQ & Tutorials

Welcome to our FAQ & Tutorials section, where we provide answers to the most frequent questions as well as links to educational resources to support your journey in genomics and bioinformatics. Explore NGS technology reviews, detailed presentations of specific NGS workflows, curated links to valuable bioinformatic tools, and other insightful publications.

Whether you’re new to the field or seeking to enhance your expertise we hope our selection offers valuable guidance. Please note that they are not exhaustive. We recommend supplementing your learning by exploring the extensive resources available on the internet.

Frequently Asked Questions

Submission of Samples

Method choice and experimental design

Bioinformatics Tutorials

Literature

Single-cell best practices

Toolkits

scrnaseq2 - The DcGC analysis pipeline for single-cell and spatial data

  • scrnaseq2 (R, QMD)
  • Written around Seurat v5
  • Follows best practices recommendations and contains additional visualizations, tables and documentation of the various analysis steps

Seurat

Alternatives to Seurat

References

Baysoy, Alev, Zhiliang Bai, Rahul Satija, and Rong Fan. 2023. “The technological landscape and applications of single-cell multi-omics.” Nature Publishing Group. https://doi.org/10.1038/s41580-023-00615-w.
Bruinsma, Stephen, Joshua Burgess, Daniel Schlingman, Agata Czyz, Natalie Morrell, Catherine Ballenger, Heather Meinholz, et al. 2018. “Bead-linked transposomes enable a normalization-free workflow for NGS library preparation.” BMC Genomics 19 (1). https://doi.org/10.1186/S12864-018-5096-9.
Eberwine, James, Jai Yoon Sul, Tamas Bartfai, and Junhyong Kim. 2014. “The promise of single-cell sequencing.” https://doi.org/10.1038/nmeth.2769.
Gunasekera, Samantha, Sam Abraham, Marc Stegger, Stanley Pang, Penghao Wang, Shafi Sahibzada, and Mark O’Dea. 2021. “Evaluating coverage bias in next-generation sequencing of Escherichia coli.” PloS One 16 (6). https://doi.org/10.1371/JOURNAL.PONE.0253440.
Gyllborg, Daniel, Christoffer Mattsson Langseth, Xiaoyan Qian, Eunkyoung Choi, Sergio Marco Salas, Markus M. Hilscher, Ed S. Lein, and Mats Nilsson. 2020. “Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue.” Nucleic Acids Research 48 (19): E112. https://doi.org/10.1093/nar/gkaa792.
Hashimshony, Tamar, Florian Wagner, Noa Sher, and Itai Yanai. 2012. “CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification.” Cell Reports. https://doi.org/10.1016/j.celrep.2012.08.003.
Kumar, Kishore R., Mark J. Cowley, and Ryan L. Davis. 2019. “Next-Generation Sequencing and Emerging Technologies.” Seminars in Thrombosis and Hemostasis 45 (7): 661–73. https://doi.org/10.1055/S-0039-1688446.
Macosko, Evan Z, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, et al. 2015. “Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.” Cell 161 (5): 1202–14. https://doi.org/10.1016/j.cell.2015.05.002.
Mardis, Elaine R. 2013. “Next-generation sequencing platforms.” Annu. Rev. Anal. Chem. (Palo Alto Calif.) 6 (June): 287–303. https://doi.org/10.1146/annurev-anchem-062012-092628.
Marx, Vivien. 2021. “Method of the Year: spatially resolved transcriptomics.” Nature Methods 2021 18:1 18 (1): 9–14. https://doi.org/10.1038/s41592-020-01033-y.
McCombie, W. Richard, John D. McPherson, and Elaine R. Mardis. 2019. “Next-Generation Sequencing Technologies.” Cold Spring Harbor Perspectives in Medicine 9 (11). https://doi.org/10.1101/CSHPERSPECT.A036798.
Rao, Anjali, Dalia Barkley, Gustavo S. França, and Itai Yanai. 2021. “Exploring tissue architecture using spatial transcriptomics.” Nature 2021 596:7871 596 (7871): 211–20. https://doi.org/10.1038/s41586-021-03634-9.
Ribarska, Teodora, Pål Marius Bjørnstad, Arvind Y. M. Sundaram, and Gregor D. Gilfillan. 2022. “Optimization of enzymatic fragmentation is crucial to maximize genome coverage: a comparison of library preparation methods for Illumina sequencing.” BMC Genomics 23 (1). https://doi.org/10.1186/S12864-022-08316-Y.
Shen, Wei, Heidi L. Sellers, Lauren A. Choate, Mariam I. Stein, Pratyush P. Tandale, Jiayu Tan, Rohit Setlem, et al. 2023. “Clinical Validation of Tagmentation-Based Genome Sequencing for Germline Disorders.” The Journal of Molecular Diagnostics : JMD 25 (7): 524–31. https://doi.org/10.1016/J.JMOLDX.2023.04.001.
Zheng, Grace X. Y., Jessica M. Terry, Phillip Belgrader, Paul Ryvkin, Zachary W. Bent, Ryan Wilson, Solongo B. Ziraldo, et al. 2017. “Massively parallel digital transcriptional profiling of single cells.” Nature Communications 8 (January): 14049. https://doi.org/10.1038/ncomms14049.