Profile picture
, 12 tweets, 3 min read Read on Twitter
I have finally updated my @nanopore basecalling comparison with the current tools! Instead of living on GitHub, it's now a proper preprint:…

Some highlights follow...
Guppy is my overall favourite. It has good accuracy and lots of features, and (if you can run it on a GPU) is blazingly fast.
Guppy's new flip-flop model is slower but more accurate. It especially does well with read-level accuracy.
Modified bases in native DNA can be a big source of consensus errors. Our main test set was K. pneumo which has Dcm methylation at the CCAGG/CCTGG motif, and most of the errors in our assemblies were in that motif.
Basecalling with a custom model trained (using Sloika) on other K. pneumo solved this problem! Dcm-related errors dropped to near zero.
Generalised conclusion: if you can train a custom model using reads from your species of interest, your basecaller will be able to handle the DNA modification in that species, giving better accuracy (especially in the consensus).
This applies to sequencing native DNA. Amplified DNA should be modification free and probably does just fine with the default basecalling models.
We also trained a model using a bigger neural network than Guppy's default model. It did a lot better in both read and consensus accuracy, but it was slow.
Generalised conclusion: Guppy's neural network architecture is making a compromise between speed and accuracy. Higher accuracy is possible if you're willing to accept slower basecalling.
If you're using Guppy and working with native DNA from Enterobacteriaceae, you should download our custom models and give them a try:…
Training custom models with Sloika wasn't easy: lots of time and effort to get the data ready, filter reads, set thresholds, control RAM usage, etc. It worked, but many @nanopore customers won't have the time or resources to do it.
So finally, a request of @nanopore: make Sloika easier to run, please! 😀 If you do, more users can train and share custom Guppy models for different organisms.
Missing some Tweet in this thread?
You can try to force a refresh.

Like this thread? Get email updates or save it to PDF!

Subscribe to Ryan Wick
Profile picture

Get real-time email alerts when new unrolls are available from this author!

This content may be removed anytime!

Twitter may remove this content at anytime, convert it as a PDF, save and print for later use!

Try unrolling a thread yourself!

how to unroll video

1) Follow Thread Reader App on Twitter so you can easily mention us!

2) Go to a Twitter thread (series of Tweets by the same owner) and mention us with a keyword "unroll" @threadreaderapp unroll

You can practice here first or read more on our help page!

Follow Us on Twitter!

Did Thread Reader help you today?

Support us! We are indie developers!

This site is made by just three indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3.00/month or $30.00/year) and get exclusive features!

Become Premium

Too expensive? Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal Become our Patreon

Thank you for your support!