Huh I remember seeing a similar thread at twitter eons ago. Is nature healing?

If you're interested in our method please check out the study and the method on github.
github.com/jaeyoungchoi...

Details of our study can be found in my previous threads from our biorxiv preprint.
bsky.app/profile/jych...

Toxin antidote system found in speciation research is good examples of this.

Topsicle can work on either Nanopore or Pacbio data. And you don't need to have a reference genome. Just get your FASTQ and analyze with Topsicle! Our package can be found on github. If you're interested in the telomere length of your organism please try!
github.com/jaeyoungchoi...

We also used our method on 8 human cancer cell lines and compared it to Telogator which is a method developed mostly for mammalian telomeres. And results shows that our method is well correlated with Telogator.

When we compare Topsicle estimates with gold standard direct estimates from Southern blots its fairly well correlated suggesting our method works pretty well. We tried our method in A. thaliana, maize, and monkeyflower and they all worked well.

Topsicle performs fairly well under simulated reads of varying sizes and error rates. Interestingly under simulated coverages we saw that the genome coverage didnt have too much of an effect on telomere length estimates

This is done by implementing a change point method. These are commonly used in electrical engineering to model signal intensity data and it also works well for our purpose. We implemented our approach into a program called Topsicle.

Because long reads can be noisy looking exact matching telomere repeat sequence (e.g. AAACCCT) can miss repeat matches. Instead we search for k-mers of different sizes to fill in the gaps. From here telomere length is measured by finding the point where theres a sudden drop in telo density

Instead we thought what about a genomics approach? Technically if a long read was sequenced from the telomere we should be able to use that read to estimate the telomere length. And thats what we did! We came up with a way to search for telomeric long reads

My lab is interested in understanding what drives the genetic variation in telomeres of plants. We are interested in telomere length variation and to study this we need to measure length of the telomere but this protocol is often difficult to implement in a typical lab. Think of Southern blots

Please give it a try if you're interested in measuring the telomere length of the organism you long read sequenced. Hopefully the peer reviewed manuscript of our method will come out shortly!

And it performs fairly well against various error rates and genome coverage. We tested it against gold standard telomere length measurements made from several A. thaliana ecotypes and found it was highly correlated with Topsicle predictions as well.

Topsicle searches for long reads from the telomere and then uses those as candidate telomere reads. Then we quantify telomere repeats with k-mer analysis and identify the telomere-subtelomere boundary using change point analysis.

Traditional way of measuring telomere length is thru Southern blot but its a lost art not many know how to do. Instead we thought what about long read sequencing since long read from telomere could be used to identify the telomere and measure its length. So we developed Topsicle. *image not related*

Telomere length is a really interesting phenotype where despite having crucial roles in maintaining genome stability its length can vary alot between individuals and even between species. Why is that? Is a major question many like to answer.