Single Molecule & Spatial Sequencing: Inspecting POD5 Files and Nanopore Mux States скачать в хорошем качестве

Single Molecule & Spatial Sequencing: Inspecting POD5 Files and Nanopore Mux States

Instructors: Theodore M. Nelson Lecture Summary: This lesson reviews the BioConda package manager, specifically referencing the miniconda implementation, as an important to manage computational pipeline dependencies. We then review the fast5 and pod5 file formats with representative examples, examining how reported metadata relates to the sequencing hardware and how to develop possible quality control statistics on this basis. The fields describing why molecules stop traversing through a Nanopore, along with the Nanopore mux switch system, are described as per-read elements output within the pod5 file. Course Summary: Sequencing-based research has become the dominant investigative practice within the biological sciences. Single-Molecule & Spatial Sequencing: Methods & Applications, responds to this development by providing a hands-on and in-depth introduction to sequencing for first year PhD and MD-PhD students, from Sanger to third-generation technologies. Utilizing an alternating lecture-lab schedule, students are introduced to fundamental basic principles of DNA & RNA science, progressing to cutting-edge library preparation and sequencing analysis techniques with Illumina and Nanopore technologies. Students will have the opportunity to perform direct-RNA sequencing samples on research samples, and experience first-hand the ethical implications of this data. Relevant concepts in biology and computer science will be addressed. GitHub Link: https://github.com/Theo-Nelson/SMS-co... Videos Referenced: https://community.nanoporetech.com/na... Relevant Packages / Papers: https://github.com/nanoporetech/pod5-... https://github.com/nanoporetech/dorado https://compgenomr.github.io/book/fas... https://nanoporetech.com/support/soft... https://github.com/hasindu2008/slow5t... Course website: https://physiology.med.cornell.edu/fa... X:   / mason_lab