@winterlichmibi.bsky.social
Reposted
Happy to introduce SegMantX. Analyzing #plasmid we find that most duplications are MGE-driven. Additional use cases include detection of DNA transfer between replicons and examination of plasmid sequence similarity. Try it out! doi.org/10.1093/molb...
SegMantX: a novel tool for detecting DNA duplications uncovers prevalent duplications in plasmids
Abstract. Segmental duplications play an important role in genome evolution via their contribution to copy-number variation, gene-family diversification an
doi.org
October 8, 2025 at 9:16 AM
Happy to introduce SegMantX. Analyzing #plasmid we find that most duplications are MGE-driven. Additional use cases include detection of DNA transfer between replicons and examination of plasmid sequence similarity. Try it out! doi.org/10.1093/molb...
Reposted
Now published in @natcomms.nature.com 🎉
www.nature.com/articles/s41...
With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!
www.nature.com/articles/s41...
With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!
September 30, 2025 at 4:21 PM
Now published in @natcomms.nature.com 🎉
www.nature.com/articles/s41...
With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!
www.nature.com/articles/s41...
With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!
Reposted
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
September 25, 2025 at 9:29 PM
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
Reposted
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
Reposted
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 4:47 AM
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
Reposted
Happy to finally share this! Read here about the best strategy the the persistence of low-copy plasmids. @mariosanter.bsky.social @iwangtoknow.bsky.social doi.org/10.1038/s414...
The combination of active partitioning and toxin-antitoxin systems is most advantageous for low-copy plasmid fitness - Nature Communications
Effe et al. evaluate how specific plasmid traits influence plasmid fitness; they provide mechanistic insight into the persistence of large conjugative plasmids, including those that disseminate antibi...
doi.org
August 3, 2025 at 10:46 AM
Happy to finally share this! Read here about the best strategy the the persistence of low-copy plasmids. @mariosanter.bsky.social @iwangtoknow.bsky.social doi.org/10.1038/s414...
Reposted
Out & #OpenAccess
📌Community outbreak of OXA-48–producing Escherichia coli linked to food premises, New Zealand, 2018-2022
doi.org/10.3201/eid3...
Thanks to folks across NZ who helped investigate & respond
#AMR #PublicHealth #Genomics #Epidemiology #Scicomm
🧵
🖥️🧬💻
#AcademicSky
#MicroSky
🧪🧫🦠
📌Community outbreak of OXA-48–producing Escherichia coli linked to food premises, New Zealand, 2018-2022
doi.org/10.3201/eid3...
Thanks to folks across NZ who helped investigate & respond
#AMR #PublicHealth #Genomics #Epidemiology #Scicomm
🧵
🖥️🧬💻
#AcademicSky
#MicroSky
🧪🧫🦠
Community Outbreak of OXA-48–Producing <em>Escherichia coli</em> Linked to Food Premises, New Zealand, 2018–2022
Outbreak of OXA-48–Producing <em>E. coli</em>, New Zealand
doi.org
July 11, 2025 at 2:52 AM
Out & #OpenAccess
📌Community outbreak of OXA-48–producing Escherichia coli linked to food premises, New Zealand, 2018-2022
doi.org/10.3201/eid3...
Thanks to folks across NZ who helped investigate & respond
#AMR #PublicHealth #Genomics #Epidemiology #Scicomm
🧵
🖥️🧬💻
#AcademicSky
#MicroSky
🧪🧫🦠
📌Community outbreak of OXA-48–producing Escherichia coli linked to food premises, New Zealand, 2018-2022
doi.org/10.3201/eid3...
Thanks to folks across NZ who helped investigate & respond
#AMR #PublicHealth #Genomics #Epidemiology #Scicomm
🧵
🖥️🧬💻
#AcademicSky
#MicroSky
🧪🧫🦠
Reposted
IMMEM is 2 months away! #MicroSky
Don't miss the opportunity to be a part of this exciting conference on microbial typing & #genomics. The theme this year, Microbial typing: from fundamental to daily microbiology
Register today and see you in Porto!
www.escmid.org/congress-eve...
Don't miss the opportunity to be a part of this exciting conference on microbial typing & #genomics. The theme this year, Microbial typing: from fundamental to daily microbiology
Register today and see you in Porto!
www.escmid.org/congress-eve...
IMMEM XIV
ESCMID in collaboration with ESGEM, is organising the 14th International Meeting on Microbial Epidemiological Markers. Discover microbial typing, from fundamental to daily microbiology in Porto, Portu...
www.escmid.org
July 11, 2025 at 8:49 AM
IMMEM is 2 months away! #MicroSky
Don't miss the opportunity to be a part of this exciting conference on microbial typing & #genomics. The theme this year, Microbial typing: from fundamental to daily microbiology
Register today and see you in Porto!
www.escmid.org/congress-eve...
Don't miss the opportunity to be a part of this exciting conference on microbial typing & #genomics. The theme this year, Microbial typing: from fundamental to daily microbiology
Register today and see you in Porto!
www.escmid.org/congress-eve...
Reposted
The new version of R for AMR is ready!
🧫 Automated antibiograms
💻 Integration to WHONET
🧪 Updated CLSI and EUCAST breakpoints
💡 Free
amr-for-r.org
#biostatistics #episky #Statistics #AMR
🧫 Automated antibiograms
💻 Integration to WHONET
🧪 Updated CLSI and EUCAST breakpoints
💡 Free
amr-for-r.org
#biostatistics #episky #Statistics #AMR
Antimicrobial Resistance Data Analysis
Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in <doi:10.1863...
amr-for-r.org
June 6, 2025 at 7:29 AM
The new version of R for AMR is ready!
🧫 Automated antibiograms
💻 Integration to WHONET
🧪 Updated CLSI and EUCAST breakpoints
💡 Free
amr-for-r.org
#biostatistics #episky #Statistics #AMR
🧫 Automated antibiograms
💻 Integration to WHONET
🧪 Updated CLSI and EUCAST breakpoints
💡 Free
amr-for-r.org
#biostatistics #episky #Statistics #AMR
Reposted
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...
Reposted
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
www.biorxiv.org/content/10.1...
Autocycler, the automated successor to Trycycler from @rrwick.bsky.social has a pre-print out - overall, pretty awesome performance (and is very easy to use)
github.com/rrwick/Autoc...
Autocycler, the automated successor to Trycycler from @rrwick.bsky.social has a pre-print out - overall, pretty awesome performance (and is very easy to use)
github.com/rrwick/Autoc...
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 ...
www.biorxiv.org
May 16, 2025 at 12:22 AM
www.biorxiv.org/content/10.1...
Autocycler, the automated successor to Trycycler from @rrwick.bsky.social has a pre-print out - overall, pretty awesome performance (and is very easy to use)
github.com/rrwick/Autoc...
Autocycler, the automated successor to Trycycler from @rrwick.bsky.social has a pre-print out - overall, pretty awesome performance (and is very easy to use)
github.com/rrwick/Autoc...
Reposted
I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
Assemblies of long-read metagenomes suffer from diverse errors
Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...
www.biorxiv.org
April 28, 2025 at 8:08 AM
I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
Reposted
So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:
rdcu.be/eg4OA
1/
rdcu.be/eg4OA
1/
Efficient and robust search of microbial genomes via phylogenetic compression
Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.
rdcu.be
April 9, 2025 at 10:27 PM
So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu
Reposted
A decade ago, we had thousands of bacterial genomes. Now, we have millions. How to scale computational methods?
Our paper in @naturemethods.bsky.social answers this: use evolutionary history to guide compression and search.
rdcu.be/eg4OA
w/ @baym.lol, @zaminiqbal.bsky.social et al. 🧵1/
Our paper in @naturemethods.bsky.social answers this: use evolutionary history to guide compression and search.
rdcu.be/eg4OA
w/ @baym.lol, @zaminiqbal.bsky.social et al. 🧵1/
April 11, 2025 at 3:01 PM
A decade ago, we had thousands of bacterial genomes. Now, we have millions. How to scale computational methods?
Our paper in @naturemethods.bsky.social answers this: use evolutionary history to guide compression and search.
rdcu.be/eg4OA
w/ @baym.lol, @zaminiqbal.bsky.social et al. 🧵1/
Our paper in @naturemethods.bsky.social answers this: use evolutionary history to guide compression and search.
rdcu.be/eg4OA
w/ @baym.lol, @zaminiqbal.bsky.social et al. 🧵1/
Reposted
Newest preprint from our lab. Congratulations to all authors!
March 15, 2025 at 3:33 PM
Newest preprint from our lab. Congratulations to all authors!
Reposted
🚀🧬 MY former colleague @micamer.bsky.social who I worked with in the early years of my career has released a BLAST service (GUI + API options) which replicates the NCBI services but with faster response times.
We would love feedback on a new NCBI-BLAST service we are launching today: sky-blast.com
Under the hood it's the same BLAST executable and databases provided by NCBI, with a replica of the NIH's interface - providing an alternative to the US gov service that's less congested, faster & more reliable
Under the hood it's the same BLAST executable and databases provided by NCBI, with a replica of the NIH's interface - providing an alternative to the US gov service that's less congested, faster & more reliable
March 12, 2025 at 1:19 AM
🚀🧬 MY former colleague @micamer.bsky.social who I worked with in the early years of my career has released a BLAST service (GUI + API options) which replicates the NCBI services but with faster response times.
Reposted
🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again!
forms.gle/YJP6WQjsk8KK...
forms.gle/YJP6WQjsk8KK...
Snippy: Microbial Variant Calling Community Survey
Help us drive the next wave of innovation in Single-Nucleotide Polymorphism (SNP) discovery and genome analysis by sharing your valuable experiences and insights. This in-depth survey aims at understa...
forms.gle
March 4, 2025 at 9:04 AM
🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again!
forms.gle/YJP6WQjsk8KK...
forms.gle/YJP6WQjsk8KK...
Reposted
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)
Reposted
Accurate and Reproducible Whole-Genome Genotyping for Bacterial Genomic Surveillance with Nanopore Sequencing Data https://www.biorxiv.org/content/10.1101/2025.02.24.639834v1
February 28, 2025 at 1:48 PM
Accurate and Reproducible Whole-Genome Genotyping for Bacterial Genomic Surveillance with Nanopore Sequencing Data https://www.biorxiv.org/content/10.1101/2025.02.24.639834v1
Reposted
The overview of AMR that you always wanted (someone else to write) - amazing!
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Antimicrobial resistance: a concise update
Antimicrobial resistance (AMR) is a serious threat to global public health, with approximately
5 million deaths associated with bacterial AMR in 2019. Tackling AMR requires a multifaceted
and cohesive...
www.thelancet.com
February 5, 2025 at 10:02 AM
The overview of AMR that you always wanted (someone else to write) - amazing!
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Truly brilliant paper with great figures! @lancetmicrobe.bsky.social
www.thelancet.com/journals/lan...
Reposted
🚨 New preprint! We know that plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by @jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14
Dissecting pOXA-48 fitness effects in clinical enterobacteria using plasmid-wide CRISPRi screens
Conjugative plasmids are the main vehicle for the spread of antimicrobial resistance (AMR) genes in clinical bacteria. AMR plasmids allow bacteria to survive antibiotic treatments, but they also produ...
www.biorxiv.org
January 24, 2025 at 12:26 PM
🚨 New preprint! We know that plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by @jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14
Reposted
📣Our latest paper is out now in mSystems: Not quite as it may seem - investigating #plasmid diversity and evolution in #Klebsiella pneumoniae at a single institution over time. A short thread 🧵 @zaminiqbal.bsky.social
January 14, 2025 at 2:20 PM
📣Our latest paper is out now in mSystems: Not quite as it may seem - investigating #plasmid diversity and evolution in #Klebsiella pneumoniae at a single institution over time. A short thread 🧵 @zaminiqbal.bsky.social
Reposted
Glad to share our preprint 🏃 **LongTrack**: long read metagenomics-based precise tracking of bacterial strains (and their genomic changes!) after 💩 fecal microbiota transplantation. A 4+ years journey and tour de force by ** @yufan01.bsky.social ** & team. A long 🧵 www.biorxiv.org/content/10.1...
December 11, 2024 at 1:51 PM
Glad to share our preprint 🏃 **LongTrack**: long read metagenomics-based precise tracking of bacterial strains (and their genomic changes!) after 💩 fecal microbiota transplantation. A 4+ years journey and tour de force by ** @yufan01.bsky.social ** & team. A long 🧵 www.biorxiv.org/content/10.1...
Reposted
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)