Who needs all bases anyway?

Chapters:

03:00 Phasing

08:50 Not Sequencing, really

14:00 Bionano Saphyr Chip

26:00 Nabsys - going electric

29:30 Tools available

39:00 QuickGen with Iuliia: Transposons!

Links:

Small explainer by CAP: https://www.cap.org/member-resources/articles/optical-genome-mapping-a-tool-with-significant-potential-from-discovery-to-diagnostics

What genome mapping can be used for: https://www.mdpi.com/2073-4425/12/3/398

Finding SVs with genome mapping: https://www.nature.com/articles/s41408-024-01059-x

Bionano github repos: https://github.com/search?q=bionano&type=repositories&s=updated&o=desc

Listen to our podcast and send your feedback to podcast[dot]explain[at]gmail[dot]com

Since 2019, West German Genome Center https://wggc.de/ operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network NGS-CN https://ngs-cn.de/ – network of NGS core facilities in Germany.

The Explain Podcast is recorded at the Multimediazentrum at Heinrich-Heine University of Düsseldorf https://www.mmz.hhu.de/ Our podcast is an outreach activity within the national genomics facility ”West German Genome Center” funded by the Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen https://www.mkw.nrw/land-foerdert-spitzenzentrum-fuer-genomsequenzierung-nordrhein-westfalen/

Chapters:

08:00 Gambling

15:00 Bubbles

30:00 Holes

57:30 One more thing

1:07:00 Finale

1:08:00 Finale of season 1!

Eric Chow explaining single cell sequencing: https://www.youtube.com/watch?v=k9VFNLLQP8c

Overview of things to consider: https://www.youtube.com/watch?v=VWUPKrnRvoQ

How to analyze single cell data: https://www.youtube.com/watch?v=5HBzgsz8qyk

A very good single cell analysis toolkit: https://satijalab.org/seurat/

Explainer for the rough workflow: https://www.technologynetworks.com/genomics/articles/understanding-single-cell-sequencing-how-it-works-and-its-applications-357578

Quick explainer on single cell sequencing: https://www.the-scientist.com/single-cell-sequencing-in-a-nutshell-71048

A method-overview paper: https://www.nature.com/articles/s12276-020-00499-2

Comparing BD Parse and 10xGenomics: https://pubmed.ncbi.nlm.nih.gov/33414681/

Pseudotime analysis: https://bioconductor.org/books/3.14/OSCA.advanced/trajectory-analysis.html

Since 2018, West German Genome Center (https://wggc.de/) operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: https://ngs-kn.de/) - network of NGS core facilities in Germany.

Listen to our podcast and send your feedback to ( podcast[dot]explain[at]gmail[dot]com ).

The Explain Podcast is recorded at the Medienlabor at Heinrich-Heine University of Düsseldorf (https://medienlab.phil.hhu.de/). Our podcast is an outreach activity within the national genomics facility "West German Genome Center" funded by the DFG (https://www.dfg.de/) (No. 407493903).

PS: I do not know how in the Parse approach the cells are treated to let the ligase and DNA enter each cell, but do not let RNA flow out of the cell at the same time. -DR

Getting the most out of Machines

Chapters:

04:30 PhiX

14:30 low complexity

19:30 UMIs

32:10 FastQC

43:00 MultiQC

56:40 PycoQC

PhiX concentrations for loading a validation run: https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000001536

Dnatech on why UMIs are used: https://dnatech.genomecenter.ucdavis.edu/faqs/what-are-umis-and-why-are-they-used-in-high-throughput-sequencing/

BMH learning on UMIs: https://www.youtube.com/watch?v=sRPMsnhIBK0

FastQC for QC of .fastq(.gz) files: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

A FastQC report from a „good“ sample: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/good_sequence_short_fastqc.html

multiqc for summarizing QC reports: https://multiqc.info/

UMI-tools for working with UMI data: https://umi-tools.readthedocs.io/en/latest/

pycoQC for Nanopore QC: https://github.com/a-slide/pycoQC

Since 2018, West German Genome Center (https://wggc.de/) operates as the next generation sequencing facility and supports research in genomics & transcriptomics by providing expertise and sequencing services. WGGC is a part of the Next Generation Sequencing Competence Network (NGS-CN: https://ngs-kn.de/) - network of NGS core facilities in Germany. Listen to our podcast and we're happy to receive your feedback&questions via Email ( podcast[dot]explain[at]gmail[dot]com ).

The Explain Podcast is recorded at the Medienlabor at Heinrich-Heine University of Düsseldorf (https://medienlab.phil.hhu.de/). Our podcast is an outreach activity within the national genomics facility "West German Genome Center" funded by the DFG (https://www.dfg.de/) (No. 407493903).