Explain Podcast

The Epigenetics Epic - Part 1

A long time coming, but here it is! Introduction: https://medlineplus.gov/genetics/understanding/howgeneswork/epigenome/Mechanisms: https://en.wikipedia.org/wiki/Epigene

454.bio

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

Special: other Nanopore Sequencing

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 QPinnacl

News: AlphaGenome, Vibecoding

Artificial Intelligence everywhere, and sometimes its useful. Correction: apparently the Biostar Handbook is not free anymore :( AlphaGenome: https://omicsomics.blogsp

News: PacBio, Illumina, Nanopore...

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-r

Array Sequencing

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/wa

Sequencing by Expansion (SBX)

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/

News: 23andMe

This time something different. Sources: https://www.23andme.com/privacy/ https://verbraucherschutzforum.berlin/2025-03-25/23andme-meldet-insolvenz-an-was-nutzer-jetzt-

Special: Sequencing in Immunology

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:

E15: Singular Genomics | ATAC-seq

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 lo

E14: Ultima Genomics + Element UltraQ

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

E13: Sequencing by Avidity | Element Biosciences + XLEAP

Because sometimes a jellyfish prevents quenching Chapters: 01:00 - XLeap update from Illumina 08:00 - Avidites start, splitting the problems 13:20 - In-depth comparis

E12: ONSO | Sequencing by binding

Now Illuminas IP, previously PacBios, previously OMNIONE... Because only one type of nucleotide is not complicated enough Chapters: 01:35 Introducing old problems 15:

Special: Long vs Short reads

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:

E11: MGI DNA Nanoball sequencing

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

E10: Genome Mapping

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 39:0

E9: Single Cell Sequencing

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: htt

Special: PhiX / UMIs / QC

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 va

E8: Nanopore

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

E7: PacBio

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 Fragme