Robert Aboukhalil
@robert.bio
Co-founder at https://omgenomics.com. Creator of https://42basepairs.com, https://sandbox.bio, https://biowasm.com, https://levelupwasm.com. Bioinformatics, genomics.
About me: https://robert.bio
About me: https://robert.bio
Reposted by Robert Aboukhalil
BINSEQ is a high-performance format for sequencing data and bqtools is a CLI tool that lets you create and manipulate these files in the style of samtools.
Excited to release a tutorial with @robert.bio showcasing how to use it to encode, decode, and grep sequences in the browser on sandbox.bio!
Excited to release a tutorial with @robert.bio showcasing how to use it to encode, decode, and grep sequences in the browser on sandbox.bio!
Efficient sequence analysis with bqtools
Interactive bqtools tutorial: learn to analyse sequence data efficiently with BINSEQ files using a command-line interface in your browser.
sandbox.bio
November 14, 2025 at 6:12 PM
BINSEQ is a high-performance format for sequencing data and bqtools is a CLI tool that lets you create and manipulate these files in the style of samtools.
Excited to release a tutorial with @robert.bio showcasing how to use it to encode, decode, and grep sequences in the browser on sandbox.bio!
Excited to release a tutorial with @robert.bio showcasing how to use it to encode, decode, and grep sequences in the browser on sandbox.bio!
Reposted by Robert Aboukhalil
Interested in learning materials to prepare undergraduate students for working with pathogens and pathogen data? I’m hosting a small curriculum development sprint/workshop. Industry/clinical and educators needed.
Please share. Apply by November 28, 2025
dnalc.cshl.edu/pdn-2026-wor...
Please share. Apply by November 28, 2025
dnalc.cshl.edu/pdn-2026-wor...
Call for Applications: Pathogen Data CUREs—Curriculum Development Workshop
dnalc.cshl.edu
November 11, 2025 at 8:29 PM
Interested in learning materials to prepare undergraduate students for working with pathogens and pathogen data? I’m hosting a small curriculum development sprint/workshop. Industry/clinical and educators needed.
Please share. Apply by November 28, 2025
dnalc.cshl.edu/pdn-2026-wor...
Please share. Apply by November 28, 2025
dnalc.cshl.edu/pdn-2026-wor...
Students often ask me how to get bioinformatics experience, and I say "projects, projects, projects!". And inevitably they say "okay but how do I find a project to do?". So I made this video with 15 project ideas:
www.youtube.com/watch?v=dfJK...
www.youtube.com/watch?v=dfJK...
15 Bioinformatics Project Ideas
YouTube video by OMGenomics
www.youtube.com
October 24, 2025 at 4:35 PM
Students often ask me how to get bioinformatics experience, and I say "projects, projects, projects!". And inevitably they say "okay but how do I find a project to do?". So I made this video with 15 project ideas:
www.youtube.com/watch?v=dfJK...
www.youtube.com/watch?v=dfJK...
Reposted by Robert Aboukhalil
New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....
October 14, 2025 at 8:48 PM
New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....
Reposted by Robert Aboukhalil
This is wonderful to play with, highly recommended for anyone who wants to understand the BWT
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
October 9, 2025 at 8:31 PM
This is wonderful to play with, highly recommended for anyone who wants to understand the BWT
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
October 9, 2025 at 5:05 PM
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
Reposted by Robert Aboukhalil
"Pro tip": If you are in a restricted environment & need quick access to a linux terminal running locally in the browser for some #bioinformatics messing around - check the sandbox.bio terminal playground. Made a bitly link for for convenience: bit.ly/bioterminal
October 6, 2025 at 10:09 AM
"Pro tip": If you are in a restricted environment & need quick access to a linux terminal running locally in the browser for some #bioinformatics messing around - check the sandbox.bio terminal playground. Made a bitly link for for convenience: bit.ly/bioterminal
Here is my deep dive into the FASTQ file format, and why you should not write Bash one-liners to parse FASTQ files: youtu.be/vFZtPTS9USE
Bioinformatics Basics: The FASTQ format and its pitfalls
YouTube video by OMGenomics
youtu.be
September 16, 2025 at 6:18 PM
Here is my deep dive into the FASTQ file format, and why you should not write Bash one-liners to parse FASTQ files: youtu.be/vFZtPTS9USE
Reposted by Robert Aboukhalil
Blogged about how zstd --long fills the gap between fast and slow-but-high-ratio genome compression methods log.bede.im/2025/09/12/z...
September 12, 2025 at 3:07 PM
Blogged about how zstd --long fills the gap between fast and slow-but-high-ratio genome compression methods log.bede.im/2025/09/12/z...
"The reference genome is essentially folded using the BWT, which allows the search for read alignments to take on a bow-tie shape in the index"
Hmmm... @benlangmead.bsky.social
Hmmm... @benlangmead.bsky.social
September 9, 2025 at 2:26 PM
"The reference genome is essentially folded using the BWT, which allows the search for read alignments to take on a bow-tie shape in the index"
Hmmm... @benlangmead.bsky.social
Hmmm... @benlangmead.bsky.social
Reposted by Robert Aboukhalil
9 CDC Directors going back to 1977 speak out. What RFK Jr has done to our nation’s public health system "should alarm every American."
It "is unlike anything we have ever seen at the agency, and unlike anything our country has ever experienced." www.nytimes.com/2025/09/01/o...
It "is unlike anything we have ever seen at the agency, and unlike anything our country has ever experienced." www.nytimes.com/2025/09/01/o...
Opinion | We Ran the C.D.C.: Kennedy Is Endangering Every American’s Health
www.nytimes.com
September 1, 2025 at 11:23 AM
9 CDC Directors going back to 1977 speak out. What RFK Jr has done to our nation’s public health system "should alarm every American."
It "is unlike anything we have ever seen at the agency, and unlike anything our country has ever experienced." www.nytimes.com/2025/09/01/o...
It "is unlike anything we have ever seen at the agency, and unlike anything our country has ever experienced." www.nytimes.com/2025/09/01/o...
Reposted by Robert Aboukhalil
From @jxtxfoundation.bsky.social | JXTX + CSHL 2025 Genome Informatics Scholarships | Up to $750 for domestic or $1,250 for international travel | Application deadline is September 15, 2025 | #OpenScience 🧬 🖥️ 🧪
⬇️
jxtxfoundation.org/news/2025-6-...
⬇️
jxtxfoundation.org/news/2025-6-...
JXTX + CSHL 2025 Genome Informatics Scholarship
JXTX + CSHL 2025 Genome Informatics Scholarships
jxtxfoundation.org
August 26, 2025 at 2:13 PM
From @jxtxfoundation.bsky.social | JXTX + CSHL 2025 Genome Informatics Scholarships | Up to $750 for domestic or $1,250 for international travel | Application deadline is September 15, 2025 | #OpenScience 🧬 🖥️ 🧪
⬇️
jxtxfoundation.org/news/2025-6-...
⬇️
jxtxfoundation.org/news/2025-6-...
There's now a race to apply AI to every imaginable field of biology. The problem is: unless you understand the biology really well, it's easy to think you've solved the problem when you haven't even come close.
youtu.be/o097zC7CM5I
youtu.be/o097zC7CM5I
AI in biology: distinguishing hype from reality
YouTube video by OMGenomics
youtu.be
August 13, 2025 at 4:00 PM
There's now a race to apply AI to every imaginable field of biology. The problem is: unless you understand the biology really well, it's easy to think you've solved the problem when you haven't even come close.
youtu.be/o097zC7CM5I
youtu.be/o097zC7CM5I
Reposted by Robert Aboukhalil
I doubt that there is a single family in America that hasn’t benefitted directly from the NIH.
July 28, 2025 at 5:37 PM
I doubt that there is a single family in America that hasn’t benefitted directly from the NIH.
Reposted by Robert Aboukhalil
Shout-out to amazing @ucsandiego.bsky.social Bioinformatics new-grads Maddie Ritter and Kyra Fetter for writing this tutorial!
Wow, sandbox.bio now provides a tutorial for viral phylogenetics that you can run right in your browser 🙌
sandbox.bio/tutorials/vi...
#microbinfie #bioinformatics #training
via @robert.bio
sandbox.bio/tutorials/vi...
#microbinfie #bioinformatics #training
via @robert.bio
sandbox.bio - Interactive bioinformatics tutorials
sandbox.bio
July 18, 2025 at 7:28 PM
Shout-out to amazing @ucsandiego.bsky.social Bioinformatics new-grads Maddie Ritter and Kyra Fetter for writing this tutorial!
💻 Just released a new tutorial: How to write a Bash script, featuring an IDE and a command-line running directly in your browser. No setup required.
sandbox.bio/tutorials/ba...
sandbox.bio/tutorials/ba...
How to write a Bash script
Interactive Bash tutorial: learn to write your own Bash scripts and process user inputs using a command-line interface in your browser.
sandbox.bio
July 18, 2025 at 2:11 PM
💻 Just released a new tutorial: How to write a Bash script, featuring an IDE and a command-line running directly in your browser. No setup required.
sandbox.bio/tutorials/ba...
sandbox.bio/tutorials/ba...
Reposted by Robert Aboukhalil
📢 Excited to share these new features on sandbox.bio:
- Python playground to quickly test code
- Customize how much memory the command-line can use! Choose between 512MB, 1GB, 2GB (previously fixed at 1GB)
- Confetti animations when you finish tutorials 🙃 (obviously the most important improvement)
- Python playground to quickly test code
- Customize how much memory the command-line can use! Choose between 512MB, 1GB, 2GB (previously fixed at 1GB)
- Confetti animations when you finish tutorials 🙃 (obviously the most important improvement)
July 1, 2025 at 4:26 PM
📢 Excited to share these new features on sandbox.bio:
- Python playground to quickly test code
- Customize how much memory the command-line can use! Choose between 512MB, 1GB, 2GB (previously fixed at 1GB)
- Confetti animations when you finish tutorials 🙃 (obviously the most important improvement)
- Python playground to quickly test code
- Customize how much memory the command-line can use! Choose between 512MB, 1GB, 2GB (previously fixed at 1GB)
- Confetti animations when you finish tutorials 🙃 (obviously the most important improvement)
🦠 New tutorial on sandbox.bio: Learn to build phylogenetic trees from viral sequences, going from multiple sequence alignment to tree generation and rooting 🧬 💻
sandbox.bio/tutorials/vi...
sandbox.bio/tutorials/vi...
Viral Phylogenetics
Interactive viral phylogenetics tutorial: learn to run multiple sequence alignment, phylogenetic inference, and tree rooting using a command-line interface in your browser.
sandbox.bio
June 26, 2025 at 3:09 PM
🦠 New tutorial on sandbox.bio: Learn to build phylogenetic trees from viral sequences, going from multiple sequence alignment to tree generation and rooting 🧬 💻
sandbox.bio/tutorials/vi...
sandbox.bio/tutorials/vi...
Reposted by Robert Aboukhalil
I also reject the notion that "most biomedical literature is unreliable/untrue." This is simply not the case. The vast majority of biomedical research is so reliable we don't even think about it. And yes, some studies and even subfields have issues, but let's acknowledge all the things that work. 🧵
"Create a journal for replication work". 🙄
This comes up time again as if there aren't existing places to put replications. PLOSOne will taken them, plenty of other journals will, and bioRxiv has had an article type called "Confirmatory Results" since we launched in 2013!
This comes up time again as if there aren't existing places to put replications. PLOSOne will taken them, plenty of other journals will, and bioRxiv has had an article type called "Confirmatory Results" since we launched in 2013!
JB plans for NIH: give grants for replication work. Create journal for replication work. Evaluate on metrics including efforts to facilitate replication, not just influence.
AH raises: funding this will take money from somewhere else. JB kind of shrugs this off but...FY2026 budget is a 40% cut.
AH raises: funding this will take money from somewhere else. JB kind of shrugs this off but...FY2026 budget is a 40% cut.
June 10, 2025 at 2:29 PM
I also reject the notion that "most biomedical literature is unreliable/untrue." This is simply not the case. The vast majority of biomedical research is so reliable we don't even think about it. And yes, some studies and even subfields have issues, but let's acknowledge all the things that work. 🧵
Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen...
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
June 10, 2025 at 4:27 PM
Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen...
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
Reposted by Robert Aboukhalil
Here's why I think there is reason to be bullish on U.S. STEM education.
doi.org/10.1093/gene...
#STEM #STEMEducation
doi.org/10.1093/gene...
#STEM #STEMEducation
There’s never been a better time to be a STEM educator
Abstract. From its current vantage point, the future of US STEM education may appear bleak. Yet STEM education's strength and importance have never been gr
doi.org
June 3, 2025 at 11:09 PM
Here's why I think there is reason to be bullish on U.S. STEM education.
doi.org/10.1093/gene...
#STEM #STEMEducation
doi.org/10.1093/gene...
#STEM #STEMEducation
Reposted by Robert Aboukhalil
Industry friends, now is the time for MUCH more speaking out on behalf of academic colleagues under duress. Here are core open source methods that many of your products doubtlessly depend on either directly or indirectly (see en.wikipedia.org/wiki/HMMER) being abruptly defunded. Make noise.
May 29, 2025 at 2:39 PM
Industry friends, now is the time for MUCH more speaking out on behalf of academic colleagues under duress. Here are core open source methods that many of your products doubtlessly depend on either directly or indirectly (see en.wikipedia.org/wiki/HMMER) being abruptly defunded. Make noise.
We always tell people to create a portfolio to showcase their work, so today we're releasing a template to get you started: github.com/omgenomics/p...
It's made for scientists & engineers who want a living resume that showcases projects, work timeline, and blog posts that demonstrate your expertise
It's made for scientists & engineers who want a living resume that showcases projects, work timeline, and blog posts that demonstrate your expertise
April 15, 2025 at 5:03 PM
We always tell people to create a portfolio to showcase their work, so today we're releasing a template to get you started: github.com/omgenomics/p...
It's made for scientists & engineers who want a living resume that showcases projects, work timeline, and blog posts that demonstrate your expertise
It's made for scientists & engineers who want a living resume that showcases projects, work timeline, and blog posts that demonstrate your expertise
Reposted by Robert Aboukhalil
Thrilled to announce the first release of the "Nanopore for Educators eBook" — nanopore4edu.org/latest/
#genomics #DNA #OxfordNanopore
#genomics #DNA #OxfordNanopore
Nanopore Network eBook
nanopore4edu.org
April 4, 2025 at 9:11 PM
Thrilled to announce the first release of the "Nanopore for Educators eBook" — nanopore4edu.org/latest/
#genomics #DNA #OxfordNanopore
#genomics #DNA #OxfordNanopore