A long time coming, but here it is!

• Introduction: https://medlineplus.gov/genetics/understanding/howgeneswork/epigenome/
• Mechanisms: https://en.wikipedia.org/wiki/Epigenetics
• DNA 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/emm201711
• DNA methylation, DNMTs and SAM: https://www.nature.com/articles/npp2012112
• Modified bases (5mC, N6-mA): https://en.wikipedia.org/wiki/DNA_methylation
• Active DNA demethylation (TET/TDG/BER): https://www.tandfonline.com/doi/full/10.1080/17501911.2025.2586452

• Bisulfite sequencing (WGBS): https://www.illumina.com/techniques/sequencing/methylation-sequencing/bisulfite-sequencing.html
• WGBS alignment benchmarking: https://www.sciencedirect.com/science/article/pii/S2001037022003853
• Illumina 5-base methylome sequencing: https://www.illumina.com/techniques/sequencing/methylation-sequencing/methylome-genome.html
• MethylationEPIC v2.0 array: https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html
• Infinium 450K datasheet: https://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet_humanmethylation450.pdf

• PacBio 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-analysis
• Nanopore sequencing accuracy: https://nanoporetech.com/platform/accuracy
• Nanopore chromatin accessibility (EPI2ME): https://epi2me.nanoporetech.com/chromatin-acc-hg002/
• Nanopore 5mC/5hmC detection: https://www.nature.com/articles/s42003-025-07681-0

• Ultima Genomics (bisulfite, EM-seq, TAPS+): https://www.ultimagenomics.com/focus-areas/methylation-profiling/
• Watchmaker TAPS+: https://www.watchmakergenomics.com/taps.html
• Element AVITI methylation sequencing: https://www.elementbiosciences.com/applications/dna-sequencing/methylation-sequencing
• MGI DNBSEQ bisulfite sequencing: https://link.springer.com/article/10.1186/s13148-023-01543-4

• NEBNext EM-seq v2: https://www.neb.com/en-us/products/e8015-nebnext-enzymatic-methyl-seq-v2-kit
• NEBNext enzymatic 5hmC-seq: https://www.neb.com/en-us/products/e3350nebnext-enzymatic-methyl-seq-5hmc-kit
• 5hmC detection overview: https://www.neb.com/en-us/products/epigenetics/methylation-analysis/5hmc-hydroxymethylation
• meCUT&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/medip
• LINE-1 global methylation assay: https://www.activemotif.com/catalog/1043/global-dna-methylation-assay-line-1
• RRBS: https://www.nature.com/articles/nprot.2010.190

• DNA 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