Sharing a flowcell, reinvented

Chapters:

- 00:00 usegalaxy.org

- 07:55 Singular Genomics start

- 21:55 Max Reads

- 29:40 DNA Structure / ATAC-seq

Setup galaxy on local hardware:

https://galaxyproject.org/admin/get-galaxy/

G4 is competing with Illumina:

https://www.genengnews.com/topics/omics/fast-and-flexible-singulars-g4-takes-aim-at-illuminas-sequencing-superiority/

Singulars chemistry is one of many:

https://www.nature.com/articles/d41586-023-00512-4

How max reads works:

https://techwriting.singulargenomics.com/max-read/Max-Read-Kit-User-Guide-600026.pdf

Small intro to DNA Structures:

https://en.wikipedia.org/wiki/Nucleic_acid_quaternary_structure

Intro to ATAC-seq:

https://www.nature.com/articles/s41596-022-00692-9

PS:

As of 2025, Singular does not advertise DNA/RNA Sequencing on their G4 anymore, but shifted to spatial data, including their G4X: https://www.singulargenomics.com/

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 ).

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Spinnin' bases on wafers to do mostly natural SBS

Chapters:

- 00:00 Ultima ePCR with beads

- 07:10 Spinning the wafer, nucleotides, no blocking

- 14:30 Ultima ppmSeq + Element UltraQ

- 25:30 How Element UltraQ was born

- 30:30 snakemake, cromwell, nextflow

- 36:50 ncRNA

Ultimas homepage: https://www.ultimagenomics.com/

Nature paper with the chemistry: https://www.nature.com/articles/s41587-022-01452-6

Elements UltraQ chemistry:

https://www.elementbiosciences.com/cloudbreak-ultraq-enhanced-sequencing-accuracy-when-precision-matters-most

Snakemake: https://snakemake.readthedocs.io/en/stable/

Nextflow: https://www.nextflow.io/docs/latest/index.html

Cromwell: https://cromwell.readthedocs.io/en/stable/

Small overview of not all ncRNA types: https://microbenotes.com/types-of-rna/

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 ).

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Because sometimes a jellyfish prevents quenching

Chapters:

01:00 - XLeap update from Illumina

08:00 - Avidites start, splitting the problems

13:20 - In-depth comparison to Illumina

22:00 - Element summary

23:30 - Bioinformatics tools: Jellyfish, KAT

25:00 - QuickGen: GWAS

Illumina about their XLeap: https://www.illumina.com/science/genomics-research/articles/data-quality-q-scores.html

Sandiegomics about element: https://sandiegomics.com/element-beats-illumina-to-the-200-genome/

Nature paper about the chemistry: https://www.nature.com/articles/s41587-023-01750-7

Jellyfish for k-mer counting: https://github.com/gmarcais/Jellyfish

GWAS Catalog: very nice data collection: https://www.ebi.ac.uk/gwas/diagram

Correcting population-based GWAS bias: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011242

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 ).

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Because only one type of nucleotide is not complicated enough

Chapters:

01:35 Introducing old problems

15:30 More Phred, more better

34:40 QuickGen: genetic testing

47:40 Bioinformatics tools: samtools

PacBio ONSO Specs: https://www.pacb.com/wp-content/uploads/Onso-specification-sheet.pdf

SBB explained by PacBio: https://www.pacb.com/blog/sbb-sequencing/

Why higher quality is better: https://pmc.ncbi.nlm.nih.gov/articles/PMC11331594/

Short read sequencing market heating up: https://www.nature.com/articles/s41587-022-01632-4

SBB for visual learners: https://www.youtube.com/watch?v=i_mSaNBOVmQ

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 ).

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Mixing up long and cheap

Chapters:

00:00:00 Intro

00:03:30 Florians history

00:13:50 Q&A Ressources for Bioinformatics

00:27:00 Long-read-tools.org

00:35:42 ONT || PacBio

00:57:00 Storage

01:09:00 Outro

Up-to-date, raw prices:https://albertvilella.substack.com/p/march-2024-ngsspecs-update

Dovetail comparing the two long-read technologies:https://dovetailbiopartners.com/2023/08/10/pacbio-vs-nanopore-unraveling-the-sequencing-odyssey-in-life-sciences/

Comparing PacBios old CLRs to ONT:https://academic.oup.com/g3journal/article/12/11/jkac192/6651842?login=true

RNA Performance comparison, wonderful read:https://www.biorxiv.org/content/10.1101/2023.07.25.550582v1.full.pdf+html

Integras 0.02$:https://www.integra-biosciences.com/united-states/en/blog/article/short-read-vs-long-read-sequencing

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 ).

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)

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Rolling in circles to make DNA yarns

Chapters:

00:00 Bioinformatics Upper Crust Tools

04:04 STAR

05:00 MGI

15:00 Daniels first contact

20:00 Brief Market Overview

22:30 Short read market

26:00 DFG High Costs Sequencing Projects Application

29:20 QuickGen: Introns and Exons

35:00 Conclusion

MGI vs Illumina: https://alitheagenomics.com/blog/how-do-rna-seq-results-compare-between-illumina-and-mgi-sequencing-platforms

Rolling the circle: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568012/pdf/nihms894568.pdf

MGI vs Illumina legal case:https://www.reuters.com/technology/illumina-ordered-pay-chinese-company-333-million-gene-sequencing-patent-case-2022-05-06/

The basics of MGIs technology: https://www.youtube.com/watch?v=gThcHHh4R0w

DFG Application:https://www.dfg.de/de/aktuelles/neuigkeiten-themen/info-wissenschaft/2024/ifw-24-30

GTL/WGGC: https://www.gtl.hhu.de/wggc

TSM link http://tsm.gtl.hhu.de/- submit your request and our colleagues will contact you

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 yourfeedback&questions via Email ( podcast[dot]explain[at]gmail[dot]com ).

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)

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

Who needs all bases anyway?

Chapters:

00:00 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 nextgeneration 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 ofDüsseldorf 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/

License Notice

This podcast including all episodes, unless otherwise noted, is licensed under a ⁠⁠⁠Creative Commons Attribution 4.0 International License⁠⁠⁠.You are free to share, remix, and use this content as long as you give appropriate credit, provide a link to the license, and indicate if changes were made.

Attribution:

Podcast Title: Explain Podcast

Creators: Iuliia Novoselova, Daniel Rickert

Website: ⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠