Ryan Wick
@rrwick.bsky.social
Bioinformatician at the Centre for Pathogen Genomics at the University of Melbourne
New blog post!
metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...
Both tools improved considerably! Time to update your conda environments 😄
metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...
Both tools improved considerably! Time to update your conda environments 😄
Benchmark update: metaMDBG and Myloasm
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
September 23, 2025 at 1:53 AM
New blog post!
metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...
Both tools improved considerably! Time to update your conda environments 😄
metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...
Both tools improved considerably! Time to update your conda environments 😄
Reposted by Ryan Wick
Excited to share our latest preprint on agtools, an open-source Python framework for analysing and manipulating assembly graphs. (1/n)
www.biorxiv.org/content/10.1...
#Bioinformatics #genomics #assembly #assemblygraphs #software
www.biorxiv.org/content/10.1...
#Bioinformatics #genomics #assembly #assemblygraphs #software
agtools: a software framework to manipulate assembly graphs
Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap information, facilitating the assembler to construct longer genomic f...
www.biorxiv.org
September 17, 2025 at 6:58 AM
Excited to share our latest preprint on agtools, an open-source Python framework for analysing and manipulating assembly graphs. (1/n)
www.biorxiv.org/content/10.1...
#Bioinformatics #genomics #assembly #assemblygraphs #software
www.biorxiv.org/content/10.1...
#Bioinformatics #genomics #assembly #assemblygraphs #software
Reposted by Ryan Wick
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 11:35 PM
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
New blog post!
I added a new feature to @gbouras13.bsky.social's Pypolca: homopolymer-only polishing. Potentially useful for cross-sample polishing - early test on Cryptosporidium looks promising.
Check it out here:
rrwick.github.io/2025/09/04/h...
I added a new feature to @gbouras13.bsky.social's Pypolca: homopolymer-only polishing. Potentially useful for cross-sample polishing - early test on Cryptosporidium looks promising.
Check it out here:
rrwick.github.io/2025/09/04/h...
Cross-sample homopolymer polishing with Pypolca
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
September 4, 2025 at 6:37 AM
New blog post!
I added a new feature to @gbouras13.bsky.social's Pypolca: homopolymer-only polishing. Potentially useful for cross-sample polishing - early test on Cryptosporidium looks promising.
Check it out here:
rrwick.github.io/2025/09/04/h...
I added a new feature to @gbouras13.bsky.social's Pypolca: homopolymer-only polishing. Potentially useful for cross-sample polishing - early test on Cryptosporidium looks promising.
Check it out here:
rrwick.github.io/2025/09/04/h...
Reposted by Ryan Wick
Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
July 30, 2025 at 2:11 AM
Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Minor new release of @nanoporetech.com's Dorado:
github.com/nanoporetech...
It supports using --bacteria when polishing an assembly with v5.2.0 data, which is nice! But if I understand correctly, it's the same bacterial polishing model from Sep 2024, not a new model.
github.com/nanoporetech...
It supports using --bacteria when polishing an assembly with v5.2.0 data, which is nice! But if I understand correctly, it's the same bacterial polishing model from Sep 2024, not a new model.
Release v1.0.1 · nanoporetech/dorado
[1.0.1] (4 June 2025)
This release introduces support in the --bacteria mode of Dorado polish for data basecalled with v5.2 models and improves the speed of 5mCG_5hmCG calling with v5.0 and v5.2 mo...
github.com
June 10, 2025 at 2:37 AM
Minor new release of @nanoporetech.com's Dorado:
github.com/nanoporetech...
It supports using --bacteria when polishing an assembly with v5.2.0 data, which is nice! But if I understand correctly, it's the same bacterial polishing model from Sep 2024, not a new model.
github.com/nanoporetech...
It supports using --bacteria when polishing an assembly with v5.2.0 data, which is nice! But if I understand correctly, it's the same bacterial polishing model from Sep 2024, not a new model.
A new long-read metagenome assembler has been released: myloasm. Very exciting! Looking forward to trying it out.
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
myloasm-docs.github.io
myloasm - metagenomic assembly with (noisy) long reads
myloasm-docs.github.io
May 29, 2025 at 5:01 AM
A new long-read metagenome assembler has been released: myloasm. Very exciting! Looking forward to trying it out.
Reposted by Ryan Wick
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
myloasm-docs.github.io
myloasm - metagenomic assembly with (noisy) long reads
myloasm-docs.github.io
May 28, 2025 at 5:54 PM
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
myloasm-docs.github.io
New blog post!
In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup.
Check it out for the full results:
rrwick.github.io/2025/05/27/d...
In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup.
Check it out for the full results:
rrwick.github.io/2025/05/27/d...
Dorado v1.0.0 and the v5.2.0 basecalling models
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
May 27, 2025 at 7:02 AM
New blog post!
In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup.
Check it out for the full results:
rrwick.github.io/2025/05/27/d...
In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup.
Check it out for the full results:
rrwick.github.io/2025/05/27/d...
New version of Dorado is out:
github.com/nanoporetech...
And for the first time in a year, this includes new DNA basecalling models!
I'll try out these new models (v5.2.0) and compare them to the previous ones (v5.0.0) in a blog post in the near future.
github.com/nanoporetech...
And for the first time in a year, this includes new DNA basecalling models!
I'll try out these new models (v5.2.0) and compare them to the previous ones (v5.0.0) in a blog post in the near future.
Release v1.0.0 · nanoporetech/dorado
[1.0.0] (21 May 2025)
We are pleased to announce the release of Dorado v1.0, delivering new models and capabilities for Oxford Nanopore data analysis. This release introduces:
New v5.2 basecalling...
github.com
May 22, 2025 at 12:07 AM
New version of Dorado is out:
github.com/nanoporetech...
And for the first time in a year, this includes new DNA basecalling models!
I'll try out these new models (v5.2.0) and compare them to the previous ones (v5.0.0) in a blog post in the near future.
github.com/nanoporetech...
And for the first time in a year, this includes new DNA basecalling models!
I'll try out these new models (v5.2.0) and compare them to the previous ones (v5.0.0) in a blog post in the near future.
New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention).
www.biorxiv.org/content/10.1...
(1/6)
www.biorxiv.org/content/10.1...
(1/6)
Autocycler: long-read consensus assembly for bacterial genomes
Motivation Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using T...
www.biorxiv.org
May 21, 2025 at 3:29 AM
New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention).
www.biorxiv.org/content/10.1...
(1/6)
www.biorxiv.org/content/10.1...
(1/6)
Reposted by Ryan Wick
Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
May 19, 2025 at 9:28 AM
Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them?
If so, you might this little project: github.com/rrwick/conda...
If so, you might this little project: github.com/rrwick/conda...
GitHub - rrwick/condaenvlist: a simple tool for listing conda environments with descriptions
a simple tool for listing conda environments with descriptions - rrwick/condaenvlist
github.com
March 27, 2025 at 4:34 AM
Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them?
If so, you might this little project: github.com/rrwick/conda...
If so, you might this little project: github.com/rrwick/conda...
New preprint is out!
We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling.
Read it here: www.biorxiv.org/content/10.1...
Data & code: github.com/rrwick/Are-r...
(1/8)
We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling.
Read it here: www.biorxiv.org/content/10.1...
Data & code: github.com/rrwick/Are-r...
(1/8)
Are reads required? High-precision variant calling from bacterial genome assemblies
Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared...
www.biorxiv.org
March 3, 2025 at 3:24 AM
New preprint is out!
We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling.
Read it here: www.biorxiv.org/content/10.1...
Data & code: github.com/rrwick/Are-r...
(1/8)
We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling.
Read it here: www.biorxiv.org/content/10.1...
Data & code: github.com/rrwick/Are-r...
(1/8)
I re-ran previous ONT basecalling benchmarks using the latest version of Dorado (thanks, @vellamike.bsky.social), and the RTX 40 series GPUs show an impressive speed boost! Check out the updated benchmark results at the bottom of this post:
rrwick.github.io/2024/08/16/s...
rrwick.github.io/2024/08/16/s...
Spring OnION: a high-spec laptop for ONT sequencing
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
February 21, 2025 at 2:56 AM
I re-ran previous ONT basecalling benchmarks using the latest version of Dorado (thanks, @vellamike.bsky.social), and the RTX 40 series GPUs show an impressive speed boost! Check out the updated benchmark results at the bottom of this post:
rrwick.github.io/2024/08/16/s...
rrwick.github.io/2024/08/16/s...
Reposted by Ryan Wick
Dorado now supports bacterial genome polishing. It can output assemblies in FASTQ, including Q scores. @rrwick.bsky.social 's analysis shows Q scores are well correlated with base call reliability, meaning they can help reduce false positives in variant calling.
rrwick.github.io/2025/02/19/f...
rrwick.github.io/2025/02/19/f...
FASTQ assemblies with Dorado polish
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
February 20, 2025 at 9:54 AM
Dorado now supports bacterial genome polishing. It can output assemblies in FASTQ, including Q scores. @rrwick.bsky.social 's analysis shows Q scores are well correlated with base call reliability, meaning they can help reduce false positives in variant calling.
rrwick.github.io/2025/02/19/f...
rrwick.github.io/2025/02/19/f...
A quick reminder: if CheckM reports an assembly as <100% complete and >0% contaminated, that doesn't necessarily mean it's incomplete or contaminated. Here are RefSeq's CheckM results for a genome I'm confident is 100% complete and 0% contaminated.
February 20, 2025 at 4:09 AM
A quick reminder: if CheckM reports an assembly as <100% complete and >0% contaminated, that doesn't necessarily mean it's incomplete or contaminated. Here are RefSeq's CheckM results for a genome I'm confident is 100% complete and 0% contaminated.
New blog post!
Ever seen a genome assembly in FASTQ format instead of FASTA? Dorado polish from @nanoporetech.com can do it, and I took a closer look:
rrwick.github.io/2025/02/19/f...
Ever seen a genome assembly in FASTQ format instead of FASTA? Dorado polish from @nanoporetech.com can do it, and I took a closer look:
rrwick.github.io/2025/02/19/f...
FASTQ assemblies with Dorado polish
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
February 19, 2025 at 5:54 AM
New blog post!
Ever seen a genome assembly in FASTQ format instead of FASTA? Dorado polish from @nanoporetech.com can do it, and I took a closer look:
rrwick.github.io/2025/02/19/f...
Ever seen a genome assembly in FASTQ format instead of FASTA? Dorado polish from @nanoporetech.com can do it, and I took a closer look:
rrwick.github.io/2025/02/19/f...
Dorado v0.9.1 now includes a bacterial model for genome polishing, so I put it to the test! How does it compare to Medaka? And does move-table data improve polishing accuracy? Read my analysis here:
rrwick.github.io/2025/02/07/d...
rrwick.github.io/2025/02/07/d...
Medaka vs Dorado polish
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
February 7, 2025 at 4:20 AM
Dorado v0.9.1 now includes a bacterial model for genome polishing, so I put it to the test! How does it compare to Medaka? And does move-table data improve polishing accuracy? Read my analysis here:
rrwick.github.io/2025/02/07/d...
rrwick.github.io/2025/02/07/d...
Do you make core genome alignments for phylogenomics? Mona Taouk and I explored how including sites with some missing data (a soft core) can improve analysis, especially for large datasets.
www.microbiologyresearch.org/content/jour...
(1/4)
www.microbiologyresearch.org/content/jour...
(1/4)
Exploring SNP filtering strategies: the influence of strict vs soft core
Phylogenetic analyses are crucial for understanding microbial evolution and infectious disease transmission. Bacterial phylogenies are often inferred from SNP alignments, with SNPs as the fundamental ...
www.microbiologyresearch.org
January 20, 2025 at 10:24 PM
Do you make core genome alignments for phylogenomics? Mona Taouk and I explored how including sites with some missing data (a soft core) can improve analysis, especially for large datasets.
www.microbiologyresearch.org/content/jour...
(1/4)
www.microbiologyresearch.org/content/jour...
(1/4)
New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
Home
A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler
github.com
December 31, 2024 at 11:43 PM
New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
New release of Canu - first one in over 3 years!
github.com/marbl/canu/r...
The notes say this will be the very last release. Many thanks to its devs Brian Walenz and @sergek.bsky.social. Canu may be a bit old and it's certainly not fast, but it makes good assemblies and so I still use it!
github.com/marbl/canu/r...
The notes say this will be the very last release. Many thanks to its devs Brian Walenz and @sergek.bsky.social. Canu may be a bit old and it's certainly not fast, but it makes good assemblies and so I still use it!
Release Canu v2.3 · marbl/canu
These are release notes for Canu version 2.3, which was released on December 17th, 2024. Canu is specialized for assembly of single-molecule sequences. Full documentation can be found at http://can...
github.com
December 17, 2024 at 8:58 PM
New release of Canu - first one in over 3 years!
github.com/marbl/canu/r...
The notes say this will be the very last release. Many thanks to its devs Brian Walenz and @sergek.bsky.social. Canu may be a bit old and it's certainly not fast, but it makes good assemblies and so I still use it!
github.com/marbl/canu/r...
The notes say this will be the very last release. Many thanks to its devs Brian Walenz and @sergek.bsky.social. Canu may be a bit old and it's certainly not fast, but it makes good assemblies and so I still use it!
Intrigued by the new dorado polish command! I'm curious how it compares to Medaka's bacterial methylation model, which I've found to be very good.
🎄 New Dorado release (v0.9.0) – and it's big!
🚀 Dorado polish command (experimental) for improving draft assemblies – faster & more accurate than Medaka
⚡ Faster modified base calling models
🔧 Usability & accuracy improvements: PolyA, Barcoding, 6mA calling
github.com/nanoporetech...
🚀 Dorado polish command (experimental) for improving draft assemblies – faster & more accurate than Medaka
⚡ Faster modified base calling models
🔧 Usability & accuracy improvements: PolyA, Barcoding, 6mA calling
github.com/nanoporetech...
Release v0.9.0 · nanoporetech/dorado
[0.9.0] (16 Dec 2024)
This major release of Dorado introduces several new features and enhancements. The polish command, currently experimental, is optimised for refining draft assemblies of human ...
github.com
December 17, 2024 at 8:35 PM
Intrigued by the new dorado polish command! I'm curious how it compares to Medaka's bacterial methylation model, which I've found to be very good.
Just had my first experience with CycloneSEQ data and shared my findings in this blog post:
rrwick.github.io/2024/12/17/c...
How does CycloneSEQ compare to @nanoporetech.com? I looked at both read-level and consensus-level accuracy. Check it out!
rrwick.github.io/2024/12/17/c...
How does CycloneSEQ compare to @nanoporetech.com? I looked at both read-level and consensus-level accuracy. Check it out!
A first look at CycloneSEQ data
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
December 16, 2024 at 9:57 PM
Just had my first experience with CycloneSEQ data and shared my findings in this blog post:
rrwick.github.io/2024/12/17/c...
How does CycloneSEQ compare to @nanoporetech.com? I looked at both read-level and consensus-level accuracy. Check it out!
rrwick.github.io/2024/12/17/c...
How does CycloneSEQ compare to @nanoporetech.com? I looked at both read-level and consensus-level accuracy. Check it out!