Ryan Wick Profile picture
Apr 23, 2020 8 tweets 2 min read Read on X
The first update to my long-read assembler benchmarking paper is up on F1000Research:
f1000research.com/articles/8-2138

Updates include...
(1/8)
The results now include fresh versions of some the assemblers: Flye (v2.6 -> v2.7), Raven (v0.0.5 -> v0.0.8) and Shasta (v0.3.0 -> v0.4.0)
(2/8)
I've also added a new assembler to the comparison: NECAT
github.com/xiaochuanle/NE…
(3/8)
A new supp figure (S11) shows the maximum indel error size in each assembly:
github.com/rrwick/Long-re…

Flye did well here: it was less likely than the other assemblers to make large-scale errors in its assemblies.
(4/8)
And various other fixes/enhancements resulting from peer review. Thanks to all the reviewers for their feedback!
(5/8)
None of my main conclusions have changed, and my favourite assemblers are still Flye, Miniasm/Minipolish and Raven, each for different reasons. If you were to twist my arm and make me choose one favourite, I think it would be Flye.
(6/8)
This update won't be the last! Newer versions of Canu (v2.0) and Raven (v1.1.5) have been released and will feature in the next version of the paper.
(7/8)
Thanks again to the @F1000Research team for facilitating this kind of living document. I've enjoyed working with them!
(8/8)

• • •

Missing some Tweet in this thread? You can try to force a refresh
 

Keep Current with Ryan Wick

Ryan Wick Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @rrwick

Jan 28, 2022
The Polypolish manuscript had graduated from preprint to peer-reviewed publication!
journals.plos.org/ploscompbiol/a…
(1/6)

See this thread for an overview:
Peer review brought quite a few improvements, so many thanks to the reviewers! My favourite addition is this new supp figure.
(2/6)
It shows that Polypolish was the tool least likely to introduce errors during polishing. It only did so at one place in 100 genomes (panel D) where it changed a 3-bp deletion to a 5-bp deletion in a tandem repeat.
(3/6)
Read 6 tweets
Jan 23, 2022
I just released a new version of Unicycler (v0.5.0) which fixes SPAdes compatibility, drops some extraneous bits and patches a few bugs.
github.com/rrwick/Unicycl…

Unicycler is now nearly 6 years old, so here's a thread with my thoughts on its place in the world in 2022.
(1/8)
Unicycler is a hybrid (short+long) bacterial genome assembly pipeline that takes a short-read-first approach. I.e. it first makes a short-read assembly graph, then uses the long reads to scaffold the graph to completion.
(2/8)
Short-read-first assembly made a lot of sense when Unicycler was first built in 2016. Back then, Nanopore reads were often shallow and low-quality, so the short-read graph made a good a starting point for assembly.
(3/8)
Read 8 tweets
Oct 18, 2021
Our preprint describing Polypolish is now up:
biorxiv.org/content/10.110…
Polypolish is a short-read polisher for long-read bacterial genome assemblies. Some highlights from the paper follow in this thread...
(1/12)
There are already quite a few short-read polishers out there: HyPo, NextPolish, ntEdit, Pilon, POLCA, Racon and wtpoa. So why did we add to this collection? It's because they nearly all suffer from the same problem with errors in repeats.
(2/12)
When you align short reads to a long-read genome assembly in the 'normal' one-alignment-per-read manner, you often get no coverage over errors in repeats. This is because reads will preferentially align to other error-free instances of the repeat.
(3/12)
Read 12 tweets
Sep 9, 2021
I've just released (during #MicroSeq2021) a new short-read polishing tool for fixing errors in long-read bacterial genome assemblies: Polypolish!
github.com/rrwick/Polypol…
(1/8)
There are many other short-read polishing tools, including HyPo, NextPolish, ntEdit, Pilon and POLCA. So what does Polypolish do differently to warrant another?
(2/8)
Most other polishers use 'normal' short-read alignments, where each read is aligned to one best location (randomly chosen in a tie). This works fine in non-repeat sequences, but errors in repeats often lead to a lack of alignments and therefore can't be fixed.
(3/8)
Read 8 tweets
Feb 22, 2021
Excited to announce a new preprint! We did a study comparing two different @nanopore library prep approaches (ligation and rapid) for bacterial genomes with small plasmids:
biorxiv.org/content/10.110…
(1/11)
I really like this paper because it has a clear conclusion simple enough to fit in a tweet: rapid preps are better than ligation preps at recovering small plasmids.
(2/11)
Figure 1 gives a simplified illustration of why we think this is the case: due to their size, small circular plasmids can avoid fragmentation during DNA extraction, leaving no ends for adapter ligation. Rapid preps, in contrast, don't depend on DNA ends.
(3/11) Image
Read 11 tweets
Sep 22, 2020
We've once again updated our paper benchmarking long-read assemblers for bacterial genomes! Take a look at the fresh results here:
f1000research.com/articles/8-2138

Updates since the last version include...
(1/9)
New versions of some assemblers: Canu v2.0, Flye v2.8, Raven v1.1.10 and Shasta v0.5.1. My favourite change here is that Flye no longer requires a genome size parameter.
(2/9)
I've also added a new assembler to the comparison: NextPolish/NextDenovo. It performed well on chromosomes but not on plasmids, and it was more cumbersome to run than the other tools.
(3/9)
Read 9 tweets

Did Thread Reader help you today?

Support us! We are indie developers!


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

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Don't want to be a Premium member but still want to support us?

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

Donate via Paypal

Or Donate anonymously using crypto!

Ethereum

0xfe58350B80634f60Fa6Dc149a72b4DFbc17D341E copy

Bitcoin

3ATGMxNzCUFzxpMCHL5sWSt4DVtS8UqXpi copy

Thank you for your support!

Follow Us!

:(