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-tech...

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.g...

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.co...

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 & tra...

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...

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...

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...

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...

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...

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...

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...

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...

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-seq...

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:...

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: h...

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...

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-adva...

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 expl...

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-st...

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/ - DNATec...

Iuliia killed the stripey cat Chapters: 00:00 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:...

H+ ions and where we can find them Chapters: 00:00 Intro 04:26 pH 08:04 DNA Polymerase reaction with H+ 12:30 Nucleotides 16:30 Homopolymer problem, but different 19:30 PCR is mean to some bases 24:30 AmpliSeq 33:40 Today’s status 38:58 cfDNA 40:00 PHRED vs Qscore 44:59 Chip scaling and prices 51:00 Outro - bitesizedbio on the technology: https://bitesizebio.com/27399/all-in-the-chip-ion-torrent-s...

If ligation is more your thing - Special Operations explaining SOLiD Sequencing: https://www.youtube.com/watch?v=YLT-DUeaLms - Writeup by the Apollo Institute on SOLiD Sequencing: https://apollo-institute.org/solid-sequencing/ - Quick run-through video by ABI: https://www.youtube.com/watch?v=nlvyF8bFDwM - Ars technica about the technology: https://arstechnica.com/science/2009/12/dna-sequencing-get...

Iuliia and Daniel have fun with salt water and alcohol Chapters: 00:00:00 DIY DNA isolation 00:15:38 Directed evolution of Enzymes DNA isolation in your kitchen - Experiment during the episode: https://www.instructables.com/How-to-Extract-Your-Own-DNA-Using-Household-Kitche/ - Another protocol with the same approach: https://learning-center.homesciencetools.com/article/how-to-extract-dna-at-home/...