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/⁠