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A long time coming, but here it is! Introduction: https://medlineplus.gov/genetics/understanding/howgeneswork/epigenome/Mechanisms: https://en.wikipedia.org/wiki/EpigeneticsDNA packaging: https://www.nature.com/scitable/topicpage/dna-packaging-nucleosomes-and-chromatin-310/Chromatin and gene regulation: https://learn.genetics.utah.edu/content/epigenetics/control/Histone writers, erasers and readers: https://www.nature.com/articles/emm201711DNA methylation, DNMTs and SAM: https://www.nature.com/articles/npp2012112Modified bases (5mC, N6-mA): https://en.wikipedia.org/wiki/DNA_methylationActive DNA demethylation (TET/TDG/BER): https://www.tandfonline.com/doi/full/10.1080/17501911.2025.2586452Bisulfite sequencing (WGBS): https://www.illumina.com/techniques/sequencing/methylation-sequencing/bisulfite-sequencing.htmlWGBS alignment benchmarking: https://www.sciencedirect.com/science/article/pii/S2001037022003853Illumina 5-base methylome sequencing: https://www.illumina.com/techniques/sequencing/methylation-sequencing/methylome-genome.htmlMethylationEPIC v2.0 array: https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.htmlInfinium 450K datasheet: https://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet_humanmethylation450.pdfPacBio HiFi methylation detection: https://www.pacb.com/revio/SMRT direct methylation detection: https://www.pacb.com/publications/direct-detection-of-dna-methylation-during-single-molecule-real-time-sequencing/Fiber-seq and cancer research: https://www.pacb.com/blog/what-a-clearer-view-of-epigenetics-can-mean-for-cancer-research/PacBio epigenetics overview: https://www.pacb.com/products-and-services/applications/epigenetics/Sequencing 101: Epigenetics: https://www.pacb.com/blog/sequencing-101-epigenetics/Oxford Nanopore modified-base calling: https://nanoporetech.com/applications/investigations/epigenetics-and-methylation-analysisNanopore sequencing accuracy: https://nanoporetech.com/platform/accuracyNanopore chromatin accessibility (EPI2ME): https://epi2me.nanoporetech.com/chromatin-acc-hg002/Nanopore 5mC/5hmC detection: https://www.nature.com/articles/s42003-025-07681-0Ultima Genomics (bisulfite, EM-seq, TAPS+): https://www.ultimagenomics.com/focus-areas/methylation-profiling/Watchmaker TAPS+: https://www.watchmakergenomics.com/taps.htmlElement AVITI methylation sequencing: https://www.elementbiosciences.com/applications/dna-sequencing/methylation-sequencingMGI DNBSEQ bisulfite sequencing: https://link.springer.com/article/10.1186/s13148-023-01543-4NEBNext EM-seq v2: https://www.neb.com/en-us/products/e8015-nebnext-enzymatic-methyl-seq-v2-kitNEBNext enzymatic 5hmC-seq: https://www.neb.com/en-us/products/e3350nebnext-enzymatic-methyl-seq-5hmc-kit5hmC detection overview: https://www.neb.com/en-us/products/epigenetics/methylation-analysis/5hmc-hydroxymethylationmeCUT&RUN: https://www.epicypher.com/product/cutana-mecutrun-kit-for-dna-methylation-sequencing/Fiber-seq chromatin profiling: https://www.epicypher.com/fiber-seq-long-read-sequencing/Fiber-seq + PacBio HiFi: https://www.pacb.com/blog/how-pairing-epicyphers-fiber-seq-with-hifi-sequencing-delivers-an-all-in-one-multiomic-view/MeDIP: https://www.activemotif.com/catalog/736/medipLINE-1 global methylation assay: https://www.activemotif.com/catalog/1043/global-dna-methylation-assay-line-1RRBS: https://www.nature.com/articles/nprot.2010.190DNA methylation biomarkers in liquid biopsies: https://www.nature.com/articles/s41388-025-03624-5 Listen to our podcast and we're happy to receive your feedback&questions via Email (podcast[dot]explain[at]gmail[dot]com ). Podcast Title: Explain Podcast Creators: Iuliia Novoselova, Daniel Rickert Website: ⁠⁠⁠⁠⁠https://ngs-cn.de/explain-podcast/⁠

The open-source DIY Sequencer was here. Update: 454.bio is now dead, but the archives still have it: https://web.archive.org/web/20250723191639/https://454.bio/ Their GitHub: https://github.com/454bio Elements new VITARI: https://www.elementbiosciences.com/products/preorder-vitari

We have the same thing at home! - yes, but in worse, cheaper or both Qitan: https://pmc.ncbi.nlm.nih.gov/articles/PMC8985760/ https://www.qitantech.com/ The QPinnacle2: https://www.vcbeathealth.com/article/1821 CycloneSEQ, the MGI-internal clone: https://en.cyclone-seq.com/nanopTech https://www.prnewswire.com/news-releases/mgi-launches-new-nanopore-sequencing-products-with-advanced-cycloneseq-technology-302241816.html https://www.biorxiv.org/content/10.1101/2024.08.19.608720v1 https://rrwick.github.io/2024/12/17/cycloneseq.html https://gigabytejournal.com/articles/154 https://gigasciencejournal.com/blog/open-cycloneseq-benchmarking-for-complete-bacterial-genomes/ Polyseq: https://polyseq.com/ Axbio: https://www.axbio.cn/products/45.html Geneus-tech: http://www.geneus-tech.com/proddetail.aspx?id=1 Nice not up-to-date table of specs: https://github.com/zhangtianyuan666/NanoporeReview2024 ONT to double promethion throughput: https://www.genomeweb.com/sequencing/jpm-oxford-nanopore-shares-plans-double-flow-cell-output-expand-menu-biopharma-market

Artificial Intelligence everywhere, and sometimes its useful. Correction: apparently the Biostar Handbook is not free anymore :( AlphaGenome: https://omicsomics.blogspot.com/2026/02/non-coding-dnas-alpha-moment.html https://www.alphagenomedocs.com/installation.html https://www.genomeweb.com/informatics/google-alphagenome-users-scrutinize-ai-models-ability-predict-variant-effects https://deepmind.google.com/science/alphagenome/ Bioinformatics Forums: Bioinformatics mistakes on Biostars: https://www.biostars.org/p/7126/ Bioinformatics stackexchange: https://bioinformatics.stackexchange.com/ Seqanswers: https://www.seqanswers.com/forum/sequencing-technologies-companies Vibecoding (current setup, top to bottom): https://claude.ai/new https://gemini.google.com/app https://duck.ai/ If danger is something you enjoy, use this: https://openclaw.ai/ YOU HAVE BEEN WARNED Paper about old LLMs that can solve simple, old and solved bioinformatics problems: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011511 Youtube has useful bioinformatics courses: 1: https://www.youtube.com/watch?v=3XFpxQF0J74&list=PLWVKUEZ25V95IKyBrxHtRTK_6Ig8Xi9-f 2: https://www.youtube.com/watch?v=LvtPXZHNoCc&list=PLeB-Dlq-v6taAXK6ZCGfqImrNWJzFt3p3

When do you get your Illumina sticker for your ONSO? This is the first part of a two-parts news roundup. PacBio News: https://aseq.substack.com/p/pacbio-sells-short-read-tech-to-illumina https://www.pacb.com/press_releases/pacbio-completes-sale-of-short-read-sequencing-assets/ https://albertvilella.substack.com/p/pacbio-sells-short-read-ip-to-illumina The 6-base sequencing run: https://www.pacb.com/wp-content/uploads/PAG-5hmC-Portik.pdf https://www.nature.com/articles/s42003-025-07681-0 ONT's P2 solo drama: https://omicsomics.blogspot.com/2026/01/p2-solo-ont-extends-support-but-not.html

For when matching and sticking is enough to get Links: Nice Youtube explainer: https://www.youtube.com/watch?v=NgRfc6atXQ8 Another nice one: https://www.youtube.com/watch?v=4bOY2Oh5tEQ Explaining this and more: https://berkeleygenomics.org/articles/How_many_human_genomes_have_been_sequenced_.html Since 2018, the West German Genome Center (⁠https://wggc.de/⁠) 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/⁠

After 454 now the second try by Roche: Axelios. Preprint: https://www.biorxiv.org/content/10.1101/2025.02.19.639056v1 Read here about the PoC: https://www.pnas.org/doi/full/10.1073/pnas.1601782113 Current state (2025): https://www.nejm.org/doi/full/10.1056/NEJMc2512825 Correction: the 5B flow cell will arrive for the NovaseqX(+), not for the Nextseq2000 Also: PacBio makes sequencing cheaper: https://www.pacb.com/press_releases/pacbio-announces-major-advances-for-revio-and-vega-to-lower-genome-cost-and-expand-multiomic-capabilities/⁠ Roche about SBX: https://sequencing.roche.com/global/en/article-listing/sequencing-platform-technologies.html Roche from a conference: https://www.youtube.com/watch?v=YN2meswiCiQ 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/⁠

This time something different. Sources: https://www.23andme.com/privacy/ https://verbraucherschutzforum.berlin/2025-03-25/23andme-meldet-insolvenz-an-was-nutzer-jetzt-wissen-sollten-357738/ https://en.wikipedia.org/wiki/23andMe_data_leak https://www.cshub.com/attacks/news/23andme-hacker-leaks-data https://www.cbsnews.com/news/dna-privacy-at-home-tests-23andme-ancestrydna-sell-data-to-third-parties/ https://techcrunch.com/2025/03/24/23andme-faces-an-uncertain-future-so-does-your-genetic-data/ https://www.theverge.com/2024/9/13/24243986/23andme-settlement-dna-data-breach-lawsuit https://newsroom.regeneron.com/news-releases/news-release-details/regeneron-enters-asset-purchase-agreement-acquire-23andmer-256/

The science of white blood cells, and much more Chapters: 05:30 Immunology how? 22:05 22q11.2 deletion syndrome 34:30 Scientific collaboration 40:00 Data losses 50:00 Flip it! 53:00 outlook 2030 Links: mini-immunology intro: https://www.youtube.com/watch?v=k9QAyP3bYmc 22Q e. V. - zentraler Anlaufpunkt für Menschen mit Deletionssyndrom 22q11 oder Duplikationssyndrom 22q11 im deutschsprachigen Raum https://www.wirsind22q.de/aus-dem-verein/vorstand Podcast for young immunologists from young immunologists https://theyoungimmunologist.buzzsprout.com/ Contact Nora here https://www.linkedin.com/in/nora-balzer-phd-253a767b Some information about training courses and events https://www.immunology.org/traininghttps://dgfi.org/dgfi-en/academy-of-immunology/ 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/⁠

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/⁠

Now Illuminas IP, previously PacBios, previously OMNIONE... 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 ... soon we need to add "vs mid-reads" 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/⁠