Paolo
@paolosonego.bsky.social
So tall, so somehow unreal, the unfathomable adults standing over us when we were small, and now they are all dead, and we look in old mirrors and see how tall and unreal and unfathomable we are now
Even to ourselves
W.E.
Even to ourselves
W.E.
Reposted by Paolo
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 Paolo
I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN.
It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package.
Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package.
Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
www.tidyverse.org
September 11, 2025 at 11:20 AM
Reposted by Paolo
From @cp-patterns.bsky.social | #Bioconductor: Planning a third decade of comprehensive support for genomic data science | #Bioinformatics #Genomics #OpenScience #OpenSource 🧬 🖥️ 🧪 🔓
⬇️
www.cell.com/patterns/ful...
⬇️
www.cell.com/patterns/ful...
Bioconductor: Planning a third decade of comprehensive support for genomic data science
This opinion piece discusses the Bioconductor project for open-source bioinformatics
and the engineering concepts underlying its effectiveness to date. Since the inception
of Bioconductor in 2002 with...
www.cell.com
September 11, 2025 at 12:58 PM
From @cp-patterns.bsky.social | #Bioconductor: Planning a third decade of comprehensive support for genomic data science | #Bioinformatics #Genomics #OpenScience #OpenSource 🧬 🖥️ 🧪 🔓
⬇️
www.cell.com/patterns/ful...
⬇️
www.cell.com/patterns/ful...
New study out: We present a deep learning + 3D vision pipeline for early-stage apple fruitlet sizing using RGB-D and YOLO. Promising results for yield prediction and orchard management. 🍎 Read here: doi.org/10.1016/j.at...
#AI #Agriculture #ComputerVision #Phenotyping
#AI #Agriculture #ComputerVision #Phenotyping
May 13, 2025 at 8:06 AM
New study out: We present a deep learning + 3D vision pipeline for early-stage apple fruitlet sizing using RGB-D and YOLO. Promising results for yield prediction and orchard management. 🍎 Read here: doi.org/10.1016/j.at...
#AI #Agriculture #ComputerVision #Phenotyping
#AI #Agriculture #ComputerVision #Phenotyping
Reposted by Paolo
New version of R is out!
Our Data Scientist, Russ Hyde, has put together a quick review of the key features and changes in R 4.5 — from new language features to graphics updates and more.
📝 Read the full blog post here: www.jumpingrivers.com/blog/whats-n...
#rstats #Rprogramming #opensource
Our Data Scientist, Russ Hyde, has put together a quick review of the key features and changes in R 4.5 — from new language features to graphics updates and more.
📝 Read the full blog post here: www.jumpingrivers.com/blog/whats-n...
#rstats #Rprogramming #opensource
What's new in R 4.5.0?
Here we summarise some of the more interesting changes that have been introduced in R 4.5.0.
www.jumpingrivers.com
April 11, 2025 at 10:34 AM
New version of R is out!
Our Data Scientist, Russ Hyde, has put together a quick review of the key features and changes in R 4.5 — from new language features to graphics updates and more.
📝 Read the full blog post here: www.jumpingrivers.com/blog/whats-n...
#rstats #Rprogramming #opensource
Our Data Scientist, Russ Hyde, has put together a quick review of the key features and changes in R 4.5 — from new language features to graphics updates and more.
📝 Read the full blog post here: www.jumpingrivers.com/blog/whats-n...
#rstats #Rprogramming #opensource
Reposted by Paolo
Do you love software engineering for exciting biological applications, open science, open source, R, Bioconductor, modern web, cloud & ML technologies?
We're looking for a software engineer to work on R/Bioconductor tools for biological data science and AI.
www.huber.embl.de/group/posts/...
We're looking for a software engineer to work on R/Bioconductor tools for biological data science and AI.
www.huber.embl.de/group/posts/...
February 14, 2025 at 9:31 AM
Do you love software engineering for exciting biological applications, open science, open source, R, Bioconductor, modern web, cloud & ML technologies?
We're looking for a software engineer to work on R/Bioconductor tools for biological data science and AI.
www.huber.embl.de/group/posts/...
We're looking for a software engineer to work on R/Bioconductor tools for biological data science and AI.
www.huber.embl.de/group/posts/...
Reposted by Paolo
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...
Reposted by Paolo
This won't be on sale till May 6th, but I got a preview copy from @darkhorse.com today! (Thanks @philipsimon.bsky.social!)
This is an expanded edition of the Eisner nominated hardcover we put out in 2019, with even more extras.
This is an expanded edition of the Eisner nominated hardcover we put out in 2019, with even more extras.
January 23, 2025 at 11:03 PM
This won't be on sale till May 6th, but I got a preview copy from @darkhorse.com today! (Thanks @philipsimon.bsky.social!)
This is an expanded edition of the Eisner nominated hardcover we put out in 2019, with even more extras.
This is an expanded edition of the Eisner nominated hardcover we put out in 2019, with even more extras.
Reposted by Paolo
I bet that a few Italians of my age or older, or younger Italians that studied the story of our industry, with DeepSeek are thinking at the computer revolution that happened in Italy thanks to a Chinese-Italian person and other very talented Italian folks: en.wikipedia.org/wiki/Mario_T...
Mario Tchou - Wikipedia
en.wikipedia.org
February 1, 2025 at 11:07 AM
I bet that a few Italians of my age or older, or younger Italians that studied the story of our industry, with DeepSeek are thinking at the computer revolution that happened in Italy thanks to a Chinese-Italian person and other very talented Italian folks: en.wikipedia.org/wiki/Mario_T...
Reposted by Paolo
If you need to sample reads (with or without replacement) from FASTQ files you may find the fastQpick utility by Joseph Rich super useful: github.com/pachterlab/f...
GitHub - pachterlab/fastQpick
Contribute to pachterlab/fastQpick development by creating an account on GitHub.
github.com
January 27, 2025 at 1:11 AM
If you need to sample reads (with or without replacement) from FASTQ files you may find the fastQpick utility by Joseph Rich super useful: github.com/pachterlab/f...
Reposted by Paolo
httr2 1.1.0 is out now: www.tidyverse.org/blog/2025/01.... Includes way better tools for streaming data (as used by ellmer.tidyverse.org), new url manipulation functions, and a _bunch_ of minor improvements and bug fixes #rstats
httr2 1.1.0 - Tidyverse
httr2 1.1.0 introduces powerful new streaming capabilities with `req_perform_connection()`, as well as comprehensive URL manipulation tools, improved AWS support, and a bunch of bug fixes.
www.tidyverse.org
January 20, 2025 at 1:44 PM
httr2 1.1.0 is out now: www.tidyverse.org/blog/2025/01.... Includes way better tools for streaming data (as used by ellmer.tidyverse.org), new url manipulation functions, and a _bunch_ of minor improvements and bug fixes #rstats
Reposted by Paolo
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)
Reposted by Paolo
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)
Reposted by Paolo
In October, I had a very long chat with Alan Moore. On magick, sci-fi, the perils of ecological doomerism, the joy of occultist pranks, the psychogeography of Stoke Newington, the invention of the taser - and much more!
As a Christmas treat here it is IN FULL.
seamas.medium.com/its-a-rabbit...
As a Christmas treat here it is IN FULL.
seamas.medium.com/its-a-rabbit...
It’s a rabbit out of a hat: On magick, fantasy and pretty much everything else, with Alan Moore
In October of this year, I spent a balmy evening talking with Alan Moore on the week that he had two — count ’em!— new books on the…
seamas.medium.com
December 23, 2024 at 1:14 PM
In October, I had a very long chat with Alan Moore. On magick, sci-fi, the perils of ecological doomerism, the joy of occultist pranks, the psychogeography of Stoke Newington, the invention of the taser - and much more!
As a Christmas treat here it is IN FULL.
seamas.medium.com/its-a-rabbit...
As a Christmas treat here it is IN FULL.
seamas.medium.com/its-a-rabbit...
Reposted by Paolo
Choose 20 films that have stayed with you or influenced you. One film per day for 20 days, in no particular order.
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 15:
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 15:
December 15, 2024 at 4:27 PM
Choose 20 films that have stayed with you or influenced you. One film per day for 20 days, in no particular order.
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 15:
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 15:
Choose 20 films that have stayed with you or influenced you. One film per day for 20 days, in no particular order.
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 14:
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 14:
December 14, 2024 at 6:16 PM
Choose 20 films that have stayed with you or influenced you. One film per day for 20 days, in no particular order.
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 14:
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 14:
Choose 20 films that have stayed with you or influenced you. One film per day for 20 days, in no particular order.
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 13:
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 13:
December 13, 2024 at 5:24 PM
Choose 20 films that have stayed with you or influenced you. One film per day for 20 days, in no particular order.
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 13:
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 13:
Choose 20 films that have stayed with you or influenced you. One film per day for 20 days, in no particular order.
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 12:
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 12:
December 12, 2024 at 4:16 PM
Choose 20 films that have stayed with you or influenced you. One film per day for 20 days, in no particular order.
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 12:
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 12:
Choose 20 films that have stayed with you or influenced you. One film per day for 20 days, in no particular order.
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 11:
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 11:
two men in military uniforms sitting in front of a world map
ALT: two men in military uniforms sitting in front of a world map
media.tenor.com
December 10, 2024 at 6:18 PM
Choose 20 films that have stayed with you or influenced you. One film per day for 20 days, in no particular order.
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 11:
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 11:
Choose 20 films that have stayed with you or influenced you. One film per day for 20 days, in no particular order.
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 10:
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 10:
December 9, 2024 at 12:53 PM
Choose 20 films that have stayed with you or influenced you. One film per day for 20 days, in no particular order.
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 10:
No explanations, no reviews, just .gifs
#Filmsky
🎥
Day 10: