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Paolo

@paolosonego.bsky.social
58 followers 429 following 46 posts

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.

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Reposted by Paolo
Rob Patro @robp.bsky.social · 06/09/2026
Gravlax 0.2.0 ships GQ, a query language for single-cell molecular evidence! Ask questions of the molecules in an experiment, per cell, per UMI class, or per aligned observation, straight from a compact .aie archive. No reads, no re-alignment, no annotation required. 🧵
A GQ query for the CD45 locus: header, three named patterns, and a pipeline that tallies which records show exon inclusion, the skip junction, or both on one observation, by sample and cell type.
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Reposted by Paolo
Rob Patro @robp.bsky.social · 27/08/2026
While we are still working on the first feature/perf full release of the rustar-aligner, you can currently use the main branch to build a byte-compatible STAR index >2x faster with <1/2 of the RAM (and use it with STAR). Plus it fixes a small STAR bug github.com/scverse/rust...
github.com
GitHub - scverse/rustar-aligner: A rust implementation of STAR
A rust implementation of STAR. Contribute to scverse/rustar-aligner development by creating an account on GitHub.
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Reposted by Paolo
Rob Patro @robp.bsky.social · 23/08/2026
The first public release of seqproc is out! 🎉 v0.1.1, powered by ANTISEQUENCE v0.1.0. seqproc let's you describe a sequencing protocol in EFGDL, compile it into a fast Rust pipeline for matching, filtering, correction, and FASTQ transformation. A powerful read pre-processing engine! 1/6
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Rob Patro @robp.bsky.social · 10/08/2026
salmon 2.5.0 is out: 28 PRs. Headline: -p is now one measured budget — gzip decode + mapping share it, and a live controller (thread-broker) solves the split from measurement instead of guessing. Quantification results unchanged; no index rebuild. github.com/COMBINE-lab/salmon 1/4
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Rob Patro @robp.bsky.social · 07/07/2026
My journey with @anthropic.com's Fable 5 model has been a very short one; characterized by "No". So, in my most recent blog post, I explain why I think "Fable is not a useful model" combine-lab.github.io/blog/2026/07...
combine-lab.github.io
COMBINE-lab - Fable is not a useful model
COMBINE-lab develops algorithms, data structures, and software for high-throughput genomics.
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Reposted by Paolo
Rob Patro @robp.bsky.social · 29/06/2026
Hey @nilshomer.com, you'd asked about this in the past: we finally got around to implementing byte-level determinism in salmon (github.com/COMBINE-lab/...). It turned out to require a lot of thought and changes, but it turns out we can do it elegantly (with RAD files) and fast (`--deterministic`)!
github.com
Release v2.2.1 · COMBINE-lab/salmon
salmon 2.2.1 The recommended 2.2.x release: it carries the full 2.2.0 feature set plus a security fix for a lz4_flex advisory pulled in by the new RAD compression. If you are on 2.2.0, upgrade. No ...
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Reposted by Paolo
Rob Patro @robp.bsky.social · 20/06/2026
If you're using salmon (esp. the new rust rewrite!) please update to the latest 2.1.1 github.com/COMBINE-lab/... ! 2.1.1 has important fixes & improvements related to decoy sequences, parallel bias correction, and reporting of library-inconsistent fragments. Thanks to github.com/BenjaminDEMA...!
github.com
Release salmon 2.1.1 · COMBINE-lab/salmon
salmon 2.1.1 A correctness-and-completeness patch on top of 2.1.0, focused on fragment-count reporting and the inferential-replicate (--numBootstraps / --numGibbsSamples) machinery: num_mapped rep...
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Reposted by Paolo
Bioconductor @bioconductor.bsky.social · 15/06/2026
📢 New package submissions to Bioconductor now go through BiocContributions. The new system uses GitHub Actions and R-universe to provide a more automated, reproducible, and streamlined review process for package authors. 📖 Read more: blog.bioconductor.org/posts/2026-0... #Bioconductor
blog.bioconductor.org
New Package Submission Process – Bioconductor community blog
The Single Package Builder (SPB) previously used for new Bioconductor package submissions has been replaced.
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Paolo @paolosonego.bsky.social · 16/06/2026
I think it's fantastic that tools like this—ones I've been using for years and consider essential in a bioinformatician's daily work—are not only being maintained, but also continuously updated and made more efficient. Thank you!
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Reposted by Paolo
Rob Patro @robp.bsky.social · 14/06/2026
salmon 2.0 (the rust re-write) is now live! It's also the version you get if you install via bioconda. This is a from-scratch rewrite in rust, and the base for future development. I'll post a more detailed thread tomorrow, but you can read the docs here combine-lab.github.io/salmon/
combine-lab.github.io
salmon
Fast, accurate transcript quantification from RNA-seq reads.
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Paolo @paolosonego.bsky.social · 15/05/2026
How to make a grown man cry #gundam : www.youtube.com/watch?v=Zt62...
youtube.com
A boy with GUNDAM | Mobile Suit Gundam 50th Anniversary - Road to 50 - Prologue Movie
YouTube video by GUNDAM CHANNEL INTL
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Reposted by Paolo
Anton Gerashchenko @antongerashchenko.bsky.social · 08/01/2026
An analysis of the situation in Iran by Navid Mohebbi, a Washington-based Iran analyst and democracy advocate: ▪️ By all measures, Day 10 has been the largest and most widespread day of Iran’s new uprising.
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Reposted by Paolo
WarTranslated (Dmitri) @wartranslated.bsky.social · 07/01/2026
Protesters in Iran have seized two cities. Residents of Abdanan and Malekshahi have pushed out security forces and are celebrating their victory.
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Reposted by Paolo
Anton Gerashchenko @antongerashchenko.bsky.social · 06/01/2026
Protests in Iran continue. Reportedly, this is the main market in Tehran.
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Reposted by Paolo
Ryan Wick @rrwick.bsky.social · 29/09/2025
Happy to share that the paper describing Autocycler is now 100% up: doi.org/10.1093/bioi... (1/3)
doi.org
Autocycler: long-read consensus assembly for bacterial genomes
AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l
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Reposted by Paolo
Ryan Wick @rrwick.bsky.social · 23/09/2025
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 😄
rrwick.github.io
Benchmark update: metaMDBG and Myloasm
a blog for miscellaneous bioinformatics stuff
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Reposted by Paolo
Thomas Lin Pedersen @thomasp85.com · 11/09/2025
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
tidyverse.org
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
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Reposted by Paolo
BF Francis Ouellette @bffo.bsky.social · 11/09/2025
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...
cell.com
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...
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Paolo @paolosonego.bsky.social · 13/05/2025
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
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Reposted by Paolo
Jumping Rivers @jumpingrivers.com · 11/04/2025
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
jumpingrivers.com
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.
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Paolo @paolosonego.bsky.social · 23/03/2025
open.spotify.com/episode/1zF0...
open.spotify.com
EP.115 - L’espansione della finanza islamica in Asia
Altri Orienti · Episode
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Paolo @paolosonego.bsky.social · 02/03/2025
open.spotify.com/episode/0nrq...
open.spotify.com
EP.113 - Tre Regni e la Cina di oggi
Altri Orienti · Episode
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Reposted by Paolo
Wolfgang Huber @wkhuber.bsky.social · 14/02/2025
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/...
Beautiful EMBL Campus in sunny Heidelberg
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Reposted by Paolo
Ryan Wick @rrwick.bsky.social · 07/02/2025
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
Medaka vs Dorado polish
a blog for miscellaneous bioinformatics stuff
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Reposted by Paolo
J.M. DeMatteis @jmdematteis.bsky.social · 23/01/2025
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.
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Reposted by Paolo
antirez @antirez.bsky.social · 01/02/2025
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...
en.wikipedia.org
Mario Tchou - Wikipedia
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Reposted by Paolo
Lior Pachter @lpachter.bsky.social · 27/01/2025
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.com
GitHub - pachterlab/fastQpick
Contribute to pachterlab/fastQpick development by creating an account on GitHub.
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Reposted by Paolo
Hadley Wickham @hadley.nz · 20/01/2025
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
tidyverse.org
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.
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Reposted by Paolo
Ryan Wick @rrwick.bsky.social · 31/12/2024
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)
github.com
Home
A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler
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Reposted by Paolo
Ryan Wick @rrwick.bsky.social · 20/01/2025
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)
microbiologyresearch.org
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 ...
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The Author, Séamas O'Reilly @seamas.bsky.social · 23/12/2024
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...
seamas.medium.com
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…
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Reposted by Paolo
Joan Cornellà @sirjoancornella.bsky.social · 24/12/2024
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Paolo @paolosonego.bsky.social · 15/12/2024
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:
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Paolo @paolosonego.bsky.social · 14/12/2024
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:
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Paolo @paolosonego.bsky.social · 13/12/2024
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:
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Paolo @paolosonego.bsky.social · 12/12/2024
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:
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Paolo @paolosonego.bsky.social · 12/12/2024
www.frontiersin.org/journals/pla...
media.tenor.com
a man in a suit and tie is standing in front of a shelf of dvds with the words #shameless self promotion above him
Alt: a man in a suit and tie is standing in front of a shelf of dvds with the words #shameless self promotion above him
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Paolo @paolosonego.bsky.social · 10/12/2024
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:
media.tenor.com
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
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Paolo @paolosonego.bsky.social · 09/12/2024
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:
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Paolo @paolosonego.bsky.social · 08/12/2024
A ‪Sala 8‬ è piaciuto il tuo post · 1g 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 9:
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Paolo @paolosonego.bsky.social · 07/12/2024
A ‪Sala 8‬ è piaciuto il tuo post · 1g 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 8:
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Paolo @paolosonego.bsky.social · 06/12/2024
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 7:
Don't watch this, I'm serious! Against the 'rules' I know but mandatory warning.
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Paolo @paolosonego.bsky.social · 05/12/2024
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 6: NM
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Paolo @paolosonego.bsky.social · 04/12/2024
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 5:
media.tenor.com
a man in a suit is sitting on a couch holding a cup of coffee and a saucer .
ALT: a man in a suit is sitting on a couch holding a cup of coffee and a saucer .
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Paolo @paolosonego.bsky.social · 03/12/2024
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 4:
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Paolo @paolosonego.bsky.social · 03/12/2024
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 3:
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Paolo @paolosonego.bsky.social · 01/12/2024
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 2:
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Paolo @paolosonego.bsky.social · 30/11/2024
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 1:
media.tenor.com
a man in a suit and tie is standing in front of a yellow curtain and giving a speech .
Alt: 92 minutes of applause
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Vincent Arel-Bundock @vincentab.bsky.social · 21/11/2024
𝚝𝚒𝚗𝚢𝚝𝚊𝚋𝚕𝚎 0.6.1 for #Rstats is out! It's an ultra simple, super flexible, and 0-dependency package to draw beautiful tables in HTML, LaTeX, Typst, Word, PDF, and PNG. And for those who ❤️ documentation, 𝚝𝚒𝚗𝚢𝚝𝚊𝚋𝚕𝚎 ships with a billion pages of tutorials: vincentarelbundock.github.io/tinytable/
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