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Ryan Wick Profile picture
@rrwick
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)

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More from @rrwick

Ryan Wick Profile picture
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
Ryan Wick Profile picture
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
Ryan Wick Profile picture
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
Ryan Wick Profile picture
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
Ryan Wick Profile picture
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
Ryan Wick Profile picture
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

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