James Ferguson
@psy-fer.bsky.social
Bioinformatician/Genomics Software Engineer @garvaninstitute.bsky.social
Views my own.
Mastodon @Psy_Fer_@genomic.social, https://genomic.social
Views my own.
Mastodon @Psy_Fer_@genomic.social, https://genomic.social
it finally happened!
I had to write a function that found the factors of a number. I was about to write a prime shortcut function too, but remembered the kmer lengths wouldn't go above 62, so i could just store those in a vector.
I had to write a function that found the factors of a number. I was about to write a prime shortcut function too, but remembered the kmer lengths wouldn't go above 62, so i could just store those in a vector.
November 10, 2025 at 2:58 AM
it finally happened!
I had to write a function that found the factors of a number. I was about to write a prime shortcut function too, but remembered the kmer lengths wouldn't go above 62, so i could just store those in a vector.
I had to write a function that found the factors of a number. I was about to write a prime shortcut function too, but remembered the kmer lengths wouldn't go above 62, so i could just store those in a vector.
Reposted by James Ferguson
jacobtomlinson.dev/posts/2025/t...
Highly relatable for anyone that has ever written a line of code used by other people
Lovely little post from @jacobtomlinson.dev
Highly relatable for anyone that has ever written a line of code used by other people
Lovely little post from @jacobtomlinson.dev
The Majority Of Your Users
The majority of your users don’t read your changelog.
The majority of your users only upgrade to new versions when forced to.
jacobtomlinson.dev
October 26, 2025 at 2:21 PM
jacobtomlinson.dev/posts/2025/t...
Highly relatable for anyone that has ever written a line of code used by other people
Lovely little post from @jacobtomlinson.dev
Highly relatable for anyone that has ever written a line of code used by other people
Lovely little post from @jacobtomlinson.dev
Not long now until our Long-Read Research Symposium on November 13th. See below the amazing line-up of speakers and talks. It's not too late to register for this free event - click the link --> www.eventbrite.com.au/e/garvan-lon...
October 27, 2025 at 4:40 AM
Not long now until our Long-Read Research Symposium on November 13th. See below the amazing line-up of speakers and talks. It's not too late to register for this free event - click the link --> www.eventbrite.com.au/e/garvan-lon...
Reposted by James Ferguson
Really exciting that the preprint on Barbell, a new demultiplexer, is finally out!
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
October 23, 2025 at 9:28 PM
Really exciting that the preprint on Barbell, a new demultiplexer, is finally out!
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
I made www.reddit.com/r/bioinforma...
I did this because the r/bioinformatics channel doesn't like talking about tools, especially if you wrote it yourself.
If you build bioinformatic tools or want to learn more about it, join the subreddit and start posting :)
I did this because the r/bioinformatics channel doesn't like talking about tools, especially if you wrote it yourself.
If you build bioinformatic tools or want to learn more about it, join the subreddit and start posting :)
bioinformaticsdev
A community for building better bioinformatics tools. Share your open-source bioinformatics tools at any stage of development - from early ideas to stable releases. Get feedback on CLI design, code ar...
www.reddit.com
October 24, 2025 at 6:56 AM
I made www.reddit.com/r/bioinforma...
I did this because the r/bioinformatics channel doesn't like talking about tools, especially if you wrote it yourself.
If you build bioinformatic tools or want to learn more about it, join the subreddit and start posting :)
I did this because the r/bioinformatics channel doesn't like talking about tools, especially if you wrote it yourself.
If you build bioinformatic tools or want to learn more about it, join the subreddit and start posting :)
Ever wanted to get the query sequence from a bam using bed coordinates?
How about the matching coordinates of an assembly mapped to a reference but repeats and SVs are confusing liftover?
Well I did while trying to benchmark STR stuff. Nice side quest.
github.com/Psy-Fer/bedp...
How about the matching coordinates of an assembly mapped to a reference but repeats and SVs are confusing liftover?
Well I did while trying to benchmark STR stuff. Nice side quest.
github.com/Psy-Fer/bedp...
GitHub - Psy-Fer/bedpull: bedpull - Pull the query sequence from bam or fasta references using a bed file
bedpull - Pull the query sequence from bam or fasta references using a bed file - Psy-Fer/bedpull
github.com
October 23, 2025 at 3:59 AM
Ever wanted to get the query sequence from a bam using bed coordinates?
How about the matching coordinates of an assembly mapped to a reference but repeats and SVs are confusing liftover?
Well I did while trying to benchmark STR stuff. Nice side quest.
github.com/Psy-Fer/bedp...
How about the matching coordinates of an assembly mapped to a reference but repeats and SVs are confusing liftover?
Well I did while trying to benchmark STR stuff. Nice side quest.
github.com/Psy-Fer/bedp...
Tried to do something simple. Didn't work. Got mad. Wrote a new tool. 😅
October 22, 2025 at 2:22 AM
Tried to do something simple. Didn't work. Got mad. Wrote a new tool. 😅
"AI" music makes my skin crawl. Like, I have a physical reaction to hearing it. Please stop 😅
October 18, 2025 at 3:50 AM
"AI" music makes my skin crawl. Like, I have a physical reaction to hearing it. Please stop 😅
Reposted by James Ferguson
Benchmark comparing SLOW5 and POD5 for nanopore raw signal data has now been published at
@GigaScience
academic.oup.com/gigascience/....
Some plots required a log scale - RAM usage and random access time.
@GigaScience
academic.oup.com/gigascience/....
Some plots required a log scale - RAM usage and random access time.
October 16, 2025 at 10:17 PM
Benchmark comparing SLOW5 and POD5 for nanopore raw signal data has now been published at
@GigaScience
academic.oup.com/gigascience/....
Some plots required a log scale - RAM usage and random access time.
@GigaScience
academic.oup.com/gigascience/....
Some plots required a log scale - RAM usage and random access time.
Reposted by James Ferguson
Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...
docs.google.com/document/d/1...
Postdoc Description.docx
Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...
docs.google.com
October 8, 2025 at 4:03 PM
Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...
docs.google.com/document/d/1...
Reposted by James Ferguson
And let’s be clear, funding discovery research is not charity, it's not just about keeping weirdos like me off the streets, IT PAYS FOR ITSELF
AAMRI/KPMG found that every $1 invested in Australian medical research returns $3.90 to the economy
AAMRI/KPMG found that every $1 invested in Australian medical research returns $3.90 to the economy
October 6, 2025 at 9:27 PM
And let’s be clear, funding discovery research is not charity, it's not just about keeping weirdos like me off the streets, IT PAYS FOR ITSELF
AAMRI/KPMG found that every $1 invested in Australian medical research returns $3.90 to the economy
AAMRI/KPMG found that every $1 invested in Australian medical research returns $3.90 to the economy
Reposted by James Ferguson
👏Translation 👏dries up 👏if you stop feeding 👏the pipeline 👏of discovery👏
#NHMRCdraftStratergy #Ihavenotes #ValueFundamentalScience
#NHMRCdraftStratergy #Ihavenotes #ValueFundamentalScience
October 6, 2025 at 9:27 PM
👏Translation 👏dries up 👏if you stop feeding 👏the pipeline 👏of discovery👏
#NHMRCdraftStratergy #Ihavenotes #ValueFundamentalScience
#NHMRCdraftStratergy #Ihavenotes #ValueFundamentalScience
Reposted by James Ferguson
Dear Everyone, I've read the #NHMRC draft strategy and I have notes ...
So I'm going to...🧵🤔🧵😱🧵😵💫🧵🙏🧵🧵🧵
This is a repost from X because you all need to know!
#NHMRCdraftStratergy #Ihavenotes #ValueFundamentalScience
@nhmrc.bsky.social
So I'm going to...🧵🤔🧵😱🧵😵💫🧵🙏🧵🧵🧵
This is a repost from X because you all need to know!
#NHMRCdraftStratergy #Ihavenotes #ValueFundamentalScience
@nhmrc.bsky.social
October 6, 2025 at 9:27 PM
Dear Everyone, I've read the #NHMRC draft strategy and I have notes ...
So I'm going to...🧵🤔🧵😱🧵😵💫🧵🙏🧵🧵🧵
This is a repost from X because you all need to know!
#NHMRCdraftStratergy #Ihavenotes #ValueFundamentalScience
@nhmrc.bsky.social
So I'm going to...🧵🤔🧵😱🧵😵💫🧵🙏🧵🧵🧵
This is a repost from X because you all need to know!
#NHMRCdraftStratergy #Ihavenotes #ValueFundamentalScience
@nhmrc.bsky.social
Reposted by James Ferguson
Adaptive sampling #WGS is moving from bench to bedside. Our work delivers SNV, structural & methylation insights on @nanoporetech.com with molecular signals emerging in minutes, not days. Watch this space 👀 #cancer #genomicAI #MultiOmics #bioinformatics @cra-chusj.bsky.social
tinyurl.com/4d337djb
tinyurl.com/4d337djb
October 7, 2025 at 1:59 AM
Adaptive sampling #WGS is moving from bench to bedside. Our work delivers SNV, structural & methylation insights on @nanoporetech.com with molecular signals emerging in minutes, not days. Watch this space 👀 #cancer #genomicAI #MultiOmics #bioinformatics @cra-chusj.bsky.social
tinyurl.com/4d337djb
tinyurl.com/4d337djb
Reposted by James Ferguson
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
www.biorxiv.org
September 22, 2025 at 5:01 PM
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
Reposted by James Ferguson
Congratulations to @hasindu2008.bsky.social form #UNSW Computer Science and Engineering for wearing a tuxedo last night 👏🏻
Also for being awarded the #EurekaPrize for outstanding early career researcher, showcase his pioneering and impacftful research in #bioinformatics software
Also for being awarded the #EurekaPrize for outstanding early career researcher, showcase his pioneering and impacftful research in #bioinformatics software
September 4, 2025 at 6:07 AM
Congratulations to @hasindu2008.bsky.social form #UNSW Computer Science and Engineering for wearing a tuxedo last night 👏🏻
Also for being awarded the #EurekaPrize for outstanding early career researcher, showcase his pioneering and impacftful research in #bioinformatics software
Also for being awarded the #EurekaPrize for outstanding early career researcher, showcase his pioneering and impacftful research in #bioinformatics software
Reposted by James Ferguson
#A-RNA2025 off to a great start. @martinalexsmith.bsky.social sharing his views on why lncRNAs should no longer be consider wallflowers.
September 1, 2025 at 4:32 AM
#A-RNA2025 off to a great start. @martinalexsmith.bsky.social sharing his views on why lncRNAs should no longer be consider wallflowers.
Just found I needed a new bit of data in an output of a tool in Rust. It involves adding to the main struct, and propagating that through all the complicated bits in the software all the way to the output writing stage.
It was pretty easy to refactor, with compiler/rust analyser. Love this language
It was pretty easy to refactor, with compiler/rust analyser. Love this language
August 29, 2025 at 6:33 AM
Just found I needed a new bit of data in an output of a tool in Rust. It involves adding to the main struct, and propagating that through all the complicated bits in the software all the way to the output writing stage.
It was pretty easy to refactor, with compiler/rust analyser. Love this language
It was pretty easy to refactor, with compiler/rust analyser. Love this language
I built and installed this absolute beast of a machine for
@nanoporetech.com
basecalling
@petermaccc.bsky.social
Threadripper
4x5090, liquid cooled
128gb DDR5 ram
~40Tb of nvme and SSD storage
TWO power supplies, a 1200W and a 2500W
All in a Corsair 9000D case
~5^7 samples/second with dorado.
@nanoporetech.com
basecalling
@petermaccc.bsky.social
Threadripper
4x5090, liquid cooled
128gb DDR5 ram
~40Tb of nvme and SSD storage
TWO power supplies, a 1200W and a 2500W
All in a Corsair 9000D case
~5^7 samples/second with dorado.
August 26, 2025 at 12:23 PM
I built and installed this absolute beast of a machine for
@nanoporetech.com
basecalling
@petermaccc.bsky.social
Threadripper
4x5090, liquid cooled
128gb DDR5 ram
~40Tb of nvme and SSD storage
TWO power supplies, a 1200W and a 2500W
All in a Corsair 9000D case
~5^7 samples/second with dorado.
@nanoporetech.com
basecalling
@petermaccc.bsky.social
Threadripper
4x5090, liquid cooled
128gb DDR5 ram
~40Tb of nvme and SSD storage
TWO power supplies, a 1200W and a 2500W
All in a Corsair 9000D case
~5^7 samples/second with dorado.
Join us for a day (Nov 13) of fascinating talks and discussions on the latest in long-read sequencing tech and related research in genomics, transcriptomics, and epigenetics. A great opportunity to network and hear from leading experts from around Aus.
www.eventbrite.com.au/e/garvan-lon...
www.eventbrite.com.au/e/garvan-lon...
Garvan Long-Read Research Symposium 2025
Join us at the Garvan Long-Read Research Symposium 2025 for a deep dive into groundbreaking discoveries in medical research!
www.eventbrite.com.au
August 15, 2025 at 5:22 AM
Join us for a day (Nov 13) of fascinating talks and discussions on the latest in long-read sequencing tech and related research in genomics, transcriptomics, and epigenetics. A great opportunity to network and hear from leading experts from around Aus.
www.eventbrite.com.au/e/garvan-lon...
www.eventbrite.com.au/e/garvan-lon...
I think I hit a new high score for basecalling speed on a 5090 machine with Dorado v1.0.2 and the v5.2.0 sup model
1.79e+07 samples/s
That's ~123gbp/day
Wow!
@nanoporetech.com have done a great job with the speedups.
1.79e+07 samples/s
That's ~123gbp/day
Wow!
@nanoporetech.com have done a great job with the speedups.
July 29, 2025 at 12:33 PM
I think I hit a new high score for basecalling speed on a 5090 machine with Dorado v1.0.2 and the v5.2.0 sup model
1.79e+07 samples/s
That's ~123gbp/day
Wow!
@nanoporetech.com have done a great job with the speedups.
1.79e+07 samples/s
That's ~123gbp/day
Wow!
@nanoporetech.com have done a great job with the speedups.
Reposted by James Ferguson
Minimod preprint by @sunethsa.bsky.social is out
biorxiv.org/content/10.1...
-similar accuracy to modkit & pb-CpG-tools.
-standard open-source licenses (NOT vendor-specific)
-Simple but faster, on a laptop ~4X for DNA and ~55X for RNA.
Code: github.com/warp9seq/min...
biorxiv.org/content/10.1...
-similar accuracy to modkit & pb-CpG-tools.
-standard open-source licenses (NOT vendor-specific)
-Simple but faster, on a laptop ~4X for DNA and ~55X for RNA.
Code: github.com/warp9seq/min...
July 23, 2025 at 9:27 AM
Minimod preprint by @sunethsa.bsky.social is out
biorxiv.org/content/10.1...
-similar accuracy to modkit & pb-CpG-tools.
-standard open-source licenses (NOT vendor-specific)
-Simple but faster, on a laptop ~4X for DNA and ~55X for RNA.
Code: github.com/warp9seq/min...
biorxiv.org/content/10.1...
-similar accuracy to modkit & pb-CpG-tools.
-standard open-source licenses (NOT vendor-specific)
-Simple but faster, on a laptop ~4X for DNA and ~55X for RNA.
Code: github.com/warp9seq/min...
Reposted by James Ferguson
If you are at #ISMB2025: Go to the
@bosc.bsky.social around 2:30pm ish where
@sunethsa.bsky.social will present real-time @nanoporetech.com frequency calculation using realfreq & standalone frequency calculation using minimod.
academic.oup.com/bioinformati...
@bosc.bsky.social around 2:30pm ish where
@sunethsa.bsky.social will present real-time @nanoporetech.com frequency calculation using realfreq & standalone frequency calculation using minimod.
academic.oup.com/bioinformati...
Realfreq: real-time base modification analysis for nanopore sequencing
AbstractSummary. Nanopore sequencers allow sequencing data to be accessed in real-time. This allows live analysis to be performed, while the sequencing is
academic.oup.com
July 21, 2025 at 8:58 AM
If you are at #ISMB2025: Go to the
@bosc.bsky.social around 2:30pm ish where
@sunethsa.bsky.social will present real-time @nanoporetech.com frequency calculation using realfreq & standalone frequency calculation using minimod.
academic.oup.com/bioinformati...
@bosc.bsky.social around 2:30pm ish where
@sunethsa.bsky.social will present real-time @nanoporetech.com frequency calculation using realfreq & standalone frequency calculation using minimod.
academic.oup.com/bioinformati...
Reposted by James Ferguson
If you are at #ISMB2025:
@bosc.bsky.social track around 2:30pm ish after
@sunethsa.bsky.social's talk, Bonson Wong will present on
nanopore basecalling on AMD GPUs using slorado
github.com/BonsonW/slor...
@bosc.bsky.social track around 2:30pm ish after
@sunethsa.bsky.social's talk, Bonson Wong will present on
nanopore basecalling on AMD GPUs using slorado
github.com/BonsonW/slor...
GitHub - BonsonW/slorado: A simplified version of Dorado built on top of S/BLOW5 format.
A simplified version of Dorado built on top of S/BLOW5 format. - BonsonW/slorado
github.com
July 21, 2025 at 9:03 AM
If you are at #ISMB2025:
@bosc.bsky.social track around 2:30pm ish after
@sunethsa.bsky.social's talk, Bonson Wong will present on
nanopore basecalling on AMD GPUs using slorado
github.com/BonsonW/slor...
@bosc.bsky.social track around 2:30pm ish after
@sunethsa.bsky.social's talk, Bonson Wong will present on
nanopore basecalling on AMD GPUs using slorado
github.com/BonsonW/slor...
Reposted by James Ferguson
We've been developing a small standalone tool for viewing & calculating frequency from modification tags in BAM files. This call is for brave users to test.
github.com/warp9seq/min...
written by
@sunethsa.bsky.social
in C, based on mod tag parsing we did for realfreq doi.org/10.1093/bioi...
github.com/warp9seq/min...
written by
@sunethsa.bsky.social
in C, based on mod tag parsing we did for realfreq doi.org/10.1093/bioi...
GitHub - warp9seq/minimod: A bioinformatics tool for viewing and calculating base modification frequencies from BAM files
A bioinformatics tool for viewing and calculating base modification frequencies from BAM files - warp9seq/minimod
github.com
July 16, 2025 at 6:16 AM
We've been developing a small standalone tool for viewing & calculating frequency from modification tags in BAM files. This call is for brave users to test.
github.com/warp9seq/min...
written by
@sunethsa.bsky.social
in C, based on mod tag parsing we did for realfreq doi.org/10.1093/bioi...
github.com/warp9seq/min...
written by
@sunethsa.bsky.social
in C, based on mod tag parsing we did for realfreq doi.org/10.1093/bioi...