Published by explain.pod
The Podcast Explain is for everyone interested in DNA/RNA sequencing or technology in general. As Iuliia doesn't have a solid background in sequencing, she keeps asking "simple" - even silly at times - questions and Daniel gives his best to make us understand.
Listen on Apple Podcasts25 min
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
38 min
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
35 min
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
24 min
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
41 min
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/
42 min
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/
21 min
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/
57 min
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/training https://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/
46 min
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/
46 min
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/
39 min
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/
54 min
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/
1 hr 11 min
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/
36 min
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/
48 min
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/
1 hr 10 min
Chapters: 00:00 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 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/
1 hr 10 min
Getting the most out of Machines Chapters: 00:00 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 supportsresearch in genomics & transcriptomics by providing expertise andsequencing 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 atHeinrich-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). 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/
57 min
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 supportsresearch in genomics & transcriptomics by providing expertise andsequencing 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 genomicsfacility "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/
56 min
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 supportsresearch in genomics & transcriptomics by providing expertise andsequencing 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 genomicsfacility "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/
38 min
Glued DNA bridges and rainbow clusters Chapters: 00:00-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 supportsresearch in genomics & transcriptomics by providing expertise andsequencing 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 1-8channels, each channel can be filled with multiple different samples- DR 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/