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).

Pushing spaghetti through holes

Chapers:

00:00 Intro

11:15 Measuring Ions

17:00 Quality

23:00 Duplex

24:30 MinION

25:15 PromethION

28:20 Methylation

29:00 Direct RNA sequencing

38:25 Basecalling

46:00 Basecalling bias

53:50 Sequencing proteins

- Nanopore explainer: https://nanoporetech.com/applications/dna-nanopore-sequencing

- Oxsci explaining the technology: https://oxsci.org/pore-over-this-advances-in-dna-sequencing/

- History of Nanopore: https://www.whatisbiotechnology.org/index.php/science/summary/nanopore/nanopore-sequencing-makes-it-possible-to-decode-the

- Shmou’s Biology explaining Nanopore sequencing: https://www.youtube.com/watch?v=MlluAjhzXqI

- A direct comparison of Nanopore and Illumina output: https://medresearch.umich.edu/office-research/about-office-research/biomedical-research-core-facilities/advanced-genomics-core/technologies/next-generation-sequencing

- A nice Nanopore QC tool we use: https://hpc.nih.gov/apps/pycoQC.html

- How a MinION looks like: https://www.whatech.com/og/markets-research/medical/658327-global-nanopore-sequencing-market-2020

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).

Zipping rounds in zeptoliters

Chapters:

00:00 Intro

07:00 Laser

09:00 Zeptoliters

13:30 Polymerase speed

19:00 Error rate

22:00 SMRT Cell

25:45 ccs

30:00 Fragment size

34:30 Megaruptor

38:20 Data flow

47:00 SVs

53:00 MAS Seq

- Starter: https://www.nature.com/articles/s41366-021-00824-3

- Karobben on PacBio sequencing: https://karobben.github.io/2023/10/30/Bioinfor/PacBio/

- bioinformticamente explaining the technology: https://bioinformaticamente.com/2020/12/05/pacbio-sequencing/

- Basic Biochem explainer of SMRT sequencing: https://www.youtube.com/watch?v=H2gUmRf-K1c

- Genomics Lab explaining it: https://www.youtube.com/watch?v=vRhUSjhygDU

- PacBio explaining BAM Tags: https://pacbiofileformats.readthedocs.io/en/13.0/BAM.html

- Megaruptor3 explainer (how we make the right sized fragments) : https://www.youtube.com/watch?v=zVhqnkQL8zo

- How we select the right sized fragments: https://www.youtube.com/watch?v=A25C8xfBbq8

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).

Glued DNA bridges and rainbow clusters

Chapters:

00:43-Flowcells

03:40-DNA glued to glass

09:00-Bridge amplification

15:50-Cluster density and patterned Flowcells

28:30-Illumina SBS summary

30:30-Limits

33:00-Multiplexing and Demultiplexing

- enseqlopedia on patterned vs unpatterned flowcell: http://enseqlopedia.com/2016/01/almost-everything-you-wanted-to-know-about-illumina-hiseq-4000-and-some-stuff-you-didnt/

- ClevaLabs on Illumina sequencing: https://www.youtube.com/watch?v=WKAUtJQ69n8

- Yourgenome on how the Illumina workflow works: https://www.yourgenome.org/facts/what-is-the-illumina-method-of-dna-sequencing/

- DNATech comparing Illumina Machines: https://dnatech.genomecenter.ucdavis.edu/illumina-high-throughput-sequencing/

- iBiology on sample preparation for Illumina sequencing: https://www.youtube.com/watch?v=PFwSe09dJX0

- StatQuest on how to use Illumina sequencing for RNA analysis: https://www.youtube.com/watch?v=tlf6wYJrwKY

- Illumina Flowcell and sequencing machines pictures: https://www.illumina.com/company/news-center/multimedia-images.html

- Nice explainer about paired-end sequencing: https://www.youtube.com/watch?v=gVrmfLXJRGM

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).

Clarification: Each Flowcell on the Illumina platform has 1-8 channels, each channel can be filled with multiple different samples - DR

Colour mixing in PHRED space

Chapters:

00:00 Nucleotides level 2

09:00 Cycles

12:00 Not-so-wobbly mutations

15:30 Reducing colourspace

22:30 Cutting connections

28:14 Costs and PHRED

- ClevaLabs on Illumina sequencing: https://www.youtube.com/watch?v=WKAUtJQ69n8

- Yourgenome on how the Illumina workflow works: https://www.yourgenome.org/facts/what-is-the-illumina-method-of-dna-sequencing/

- DNATech comparing Illumina Machines: https://dnatech.genomecenter.ucdavis.edu/illumina-high-throughput-sequencing/

- iBiology on sample preparation for Illumina sequencing: https://www.youtube.com/watch?v=PFwSe09dJX0

- StatQuest on how to use Illumina sequencing for RNA analysis: https://www.youtube.com/watch?v=tlf6wYJrwKY

- Illumina Flowcell and sequencing machines pictures: https://www.illumina.com/company/news-center/multimedia-images.html

- Nice explainer about paired-end sequencing: https://www.youtube.com/watch?v=gVrmfLXJRGM

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).

CORRECTION: On the Illumina 1-channel chemistry, one base signal gets added, one removed at the enzymatic step: so that's one signal that stays, one that disappears, one that comes to shine and one that never shines. - DR

Iuliia killed the stripey cat

Chapters:

00:01:00 Intro

00:04:44 Stripes

00:11:40 Sanger with colors

00:17:20 CATCATCAT...

00:33:20 Planes

00:38:15 Genome assembly

00:40:00 Transcriptomics

01:01:00 Hi-C

Why women are stripey: https://www.youtube.com/watch?v=BD6h-wDj7bw

Future-science about str profiling: https://www.future-science.com/doi/10.2144/000112582

Mark Santucci explaining str profiles: https://www.youtube.com/watch?v=Eg3gH2wmAW8

NIJ explaining the theory for beginners: https://nij.ojp.gov/topics/articles/what-str-analysis

MIT on genome assembly: https://www.youtube.com/watch?v=ZYW2AeDE6wU

Fundamentals of genome assembly by Bioinformatics DotCa: https://www.youtube.com/watch?v=5wvGapmA5zM

Genome assembly tips from F1000Research: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850084/

CD Genomics explaining some genome assembly metrics: https://www.cd-genomics.com/an-overview-of-genome-assembly.html

Geneticeducation giving an intro to transcriptomics: https://geneticeducation.co.in/what-is-transcriptomics/

A slideshare explaining transcriptomics: https://www.slideshare.net/divyasrivastava17/transcriptome-analysis

How to create a volcano plot in R: https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot-r/tutorial.html

Bioinformatic walk-through by the galaxy project with a typical RNA-Seq experiment: https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html

RNA splicing explained by arpan: https://www.youtube.com/watch?v=IJQv1H-2IoI

khanacademy on RNA processing: https://www.khanacademy.org/science/ap-biology/gene-expression-and-regulation/transcription-and-rna-processing/a/eukaryotic-pre-mrna-processing

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).