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

See this thread for an overview:

https://twitter.com/rrwick/status/1449939336263188489

Peer review brought quite a few improvements, so many thanks to the reviewers! My favourite addition is this new supp figure.
(2/6)

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)

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)

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)

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)

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'm releasing a new tool today: Trycycler!
github.com/rrwick/Trycycl…

It is for generating a consensus long-read assembly of a bacterial genome.

(1/9) I.e. you give Trycycler multiple different long-read assemblies of the same genome, and it produces a single consensus assembly that is better than any of the inputs.

(2/9)

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)

New paper for the new year! It compares different long-read assemblers for microbial genome assembly:
f1000research.com/articles/8-213…

Two Twitter threads follow - one about the paper itself and one about my experience with @F1000Research.
(1/n) In this paper, we did a ton of long-read microbial genome assemblies (using both real and simulated long-read sets) to see how the current assemblers perform.
(2/5)

I've got a little new tool to share: Minipolish
github.com/rrwick/Minipol…

It does Racon-polishing on a miniasm long-read assembly. Why not just use Racon directly? For a few reasons...

(1/6) 1. Minipolish keeps the assembly in graph form (GFA format) whereas Racon produces FASTA sequences.

2. Racon has a nasty habit of sometimes truncating sequences a little bit when it polishes them - Minipolish will repair this.

(2/6)

I have a little tool to share, in case it's useful to anybody else:
github.com/rrwick/Assembl…

Nothing too fancy, but if you work with large numbers of bacterial genomes, read on... (1/9) I occasionally encounter a situation where I have lots of genome assemblies, but some are quite redundant. Often because the set contains outbreaks of near-identical genomes. (2/9)

I've just put together a quick addendum to our recent @nanopore basecalling paper, looking at different Guppy models and polishing strategies:
github.com/rrwick/August-…

It's not long, but if you'd prefer a Twitter-based summary... (1/9) This was our recent paper on basecalling accuracy:
genomebiology.biomedcentral.com/articles/10.11…

It looked at the performance of basecallers over time and examined both read-level and consensus-level accuracy. (2/9)

Guillaume (@phylogeo) has just posted a new paper that we've been working on!
biorxiv.org/content/10.110…

He already summarised it well, so take a look at his thread for an overview:

https://twitter.com/phylogeo/status/1153833032689672193

I only had a few thoughts to add... (1/9) One of the big conclusions is that using more genomes is better when building metagenomic classification databases. More genomes = bigger species pan genomes = better ability to assign reads to a species. (2/9)

Our analysis of @nanopore basecalling performance started life as a GitHub repo, and after pupating on bioRxiv for a while, it has now emerged as a manuscript in Genome Biology!
genomebiology.biomedcentral.com/articles/10.11…

Some highlights and discussion (and requests of @nanopore) to follow... Guppy is a very nice basecaller and it continues to get better as features are added. For 99.9% of users, this is probably the only basecaller they need.

I have finally updated my @nanopore basecalling comparison with the current tools! Instead of living on GitHub, it's now a proper preprint:
biorxiv.org/content/10.110…

Some highlights follow...
(1/12) 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.
(2/12)

I've added a section on Medaka polishing to my Basecalling comparison. It did improve assemblies, but not as much as Nanopolish.
github.com/rrwick/Basecal… I also tried a combination of Medaka and Nanopolish (in both orders), but could not improve upon Nanopolish alone.