Dan Portik
@dportik.bsky.social
Bioinformatics scientist at PacBio. I currently work on metagenomics and methylation, but previously studied phylogenomics and frog/lizard evolution.
🦠 🐸 🦎 🧬
Free time: climbing 🧗, curling 🥌, and plants 🪴🌵.
🦠 🐸 🦎 🧬
Free time: climbing 🧗, curling 🥌, and plants 🪴🌵.
Reposted by Dan Portik
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning - Nature Biotechnology
PlasMAAG uses cross-sample information to improve plasmid reconstruction from metagenomic samples.
www.nature.com
February 4, 2026 at 8:20 PM
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
Reposted by Dan Portik
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... 🧬💻🧪 github.com/RasmussenLab...
February 5, 2026 at 5:02 PM
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... 🧬💻🧪 github.com/RasmussenLab...
Reposted by Dan Portik
New Preprint 📢 from our team 🔎 Critical assessment of #intratumor and #low #biomass #microbiome using #longread sequencing
Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very low-microbe tissue samples, how much 1/
Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very low-microbe tissue samples, how much 1/
February 5, 2026 at 1:15 PM
New Preprint 📢 from our team 🔎 Critical assessment of #intratumor and #low #biomass #microbiome using #longread sequencing
Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very low-microbe tissue samples, how much 1/
Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very low-microbe tissue samples, how much 1/
I keep a giant table of long-read metagenomics tools for different applications and update it as new ones appear. It's hard to keep up with these days!
If I didn't have that, I would have already forgotten about it 😅
If I didn't have that, I would have already forgotten about it 😅
January 28, 2026 at 9:52 PM
I keep a giant table of long-read metagenomics tools for different applications and update it as new ones appear. It's hard to keep up with these days!
If I didn't have that, I would have already forgotten about it 😅
If I didn't have that, I would have already forgotten about it 😅
I think Single-M was written with that use-case in mind. Haven't tested it personally so can't vouch for it, but likely worth a try.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper - Nature Biotechnology
Novel microbial species in metagenomes are identified using conserved regions within universal marker genes.
www.nature.com
January 28, 2026 at 9:41 PM
I think Single-M was written with that use-case in mind. Haven't tested it personally so can't vouch for it, but likely worth a try.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
There are a few tools out there, this being one of the more recent ones:
doi.org/10.1101/2025...
I think there are some other alternatives listed in there as well.
I haven't personally tested it but would love to hear your feedback if you do.
doi.org/10.1101/2025...
I think there are some other alternatives listed in there as well.
I haven't personally tested it but would love to hear your feedback if you do.
doi.org
January 28, 2026 at 9:39 PM
There are a few tools out there, this being one of the more recent ones:
doi.org/10.1101/2025...
I think there are some other alternatives listed in there as well.
I haven't personally tested it but would love to hear your feedback if you do.
doi.org/10.1101/2025...
I think there are some other alternatives listed in there as well.
I haven't personally tested it but would love to hear your feedback if you do.
Reposted by Dan Portik
🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and
@titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ?
doi.org/10.1093/narg...
@titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ?
doi.org/10.1093/narg...
Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations
Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru
doi.org
December 9, 2025 at 3:25 AM
🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and
@titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ?
doi.org/10.1093/narg...
@titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ?
doi.org/10.1093/narg...
To simplify - you took the annual estimate of consumable revenue for all Revio instruments in the field, and tried to make that number fit with the Q3 consumable revenue (which is only ~25% of the consumable revenue for the year).
November 6, 2025 at 7:06 PM
To simplify - you took the annual estimate of consumable revenue for all Revio instruments in the field, and tried to make that number fit with the Q3 consumable revenue (which is only ~25% of the consumable revenue for the year).
The 21.3M is just for Q3 - you'd need to add up consumable revenue from Q1, Q2, and estimate for Q4 to get an annual estimate of consumable revenue.
The estimate of annual consumable revenue of 236k per Revio system x 310 systems = ~73M, but we know utilization differs across users.
The estimate of annual consumable revenue of 236k per Revio system x 310 systems = ~73M, but we know utilization differs across users.
November 6, 2025 at 6:40 PM
The 21.3M is just for Q3 - you'd need to add up consumable revenue from Q1, Q2, and estimate for Q4 to get an annual estimate of consumable revenue.
The estimate of annual consumable revenue of 236k per Revio system x 310 systems = ~73M, but we know utilization differs across users.
The estimate of annual consumable revenue of 236k per Revio system x 310 systems = ~73M, but we know utilization differs across users.
I don't think any Vega consumable numbers were included here, but I could be wrong. It might be that Vega estimates will be given after this year, giving a bigger time window to measure various metrics following the launch of the platform.
November 6, 2025 at 6:16 PM
I don't think any Vega consumable numbers were included here, but I could be wrong. It might be that Vega estimates will be given after this year, giving a bigger time window to measure various metrics following the launch of the platform.
I'd argue that:
"PacBio sequencing ** has historically been** done by large service centres with large queues and substantial turnaround times"...
but that's starting to change now.
You are waiting for evidence that Vega is driving that, and that's a fair point.
"PacBio sequencing ** has historically been** done by large service centres with large queues and substantial turnaround times"...
but that's starting to change now.
You are waiting for evidence that Vega is driving that, and that's a fair point.
November 5, 2025 at 6:35 PM
I'd argue that:
"PacBio sequencing ** has historically been** done by large service centres with large queues and substantial turnaround times"...
but that's starting to change now.
You are waiting for evidence that Vega is driving that, and that's a fair point.
"PacBio sequencing ** has historically been** done by large service centres with large queues and substantial turnaround times"...
but that's starting to change now.
You are waiting for evidence that Vega is driving that, and that's a fair point.
Revio is a great product - it dramatically increased throughput over Sequel II (3x more data per cell, 12x more data per fully loaded run) and dropped the cost substantially. It's been the most successful instrument launch for the company, and now PacBio sequencing is at an all time high.
November 5, 2025 at 5:59 PM
Revio is a great product - it dramatically increased throughput over Sequel II (3x more data per cell, 12x more data per fully loaded run) and dropped the cost substantially. It's been the most successful instrument launch for the company, and now PacBio sequencing is at an all time high.
I'd encourage you to listen in on the PacBio Q3 results, which can tell you more about instrument sales, consumable usage, etc.
investor.pacificbiosciences.com/news-release...
investor.pacificbiosciences.com/news-release...
PacBio to Report Third Quarter 2025 Financial Results on November 5, 2025 | PacBio
The Investor Relations website contains information about PacBio's business for stockholders, potential investors, and financial analysts.
investor.pacificbiosciences.com
November 5, 2025 at 5:46 PM
I'd encourage you to listen in on the PacBio Q3 results, which can tell you more about instrument sales, consumable usage, etc.
investor.pacificbiosciences.com/news-release...
investor.pacificbiosciences.com/news-release...
I'm still only talking about PacBio here, not other technologies.
PacBio sequencing is now available in individual labs (not just sequencing cores), and does not require months of waiting.
You can continue to advertise other technologies if you'd like, but it's a distraction from the main point.
PacBio sequencing is now available in individual labs (not just sequencing cores), and does not require months of waiting.
You can continue to advertise other technologies if you'd like, but it's a distraction from the main point.
November 5, 2025 at 5:41 PM
I'm still only talking about PacBio here, not other technologies.
PacBio sequencing is now available in individual labs (not just sequencing cores), and does not require months of waiting.
You can continue to advertise other technologies if you'd like, but it's a distraction from the main point.
PacBio sequencing is now available in individual labs (not just sequencing cores), and does not require months of waiting.
You can continue to advertise other technologies if you'd like, but it's a distraction from the main point.
Hi David, I'm discussing PacBio here.
Vega solves the problem you stated:
"PacBio sequencing is typically done by large service centres with large queues and substantial turnaround times, often measured in weeks or months."
Getting a machine in the lab means HiFi data in a day.
Vega solves the problem you stated:
"PacBio sequencing is typically done by large service centres with large queues and substantial turnaround times, often measured in weeks or months."
Getting a machine in the lab means HiFi data in a day.
November 4, 2025 at 8:14 PM
Hi David, I'm discussing PacBio here.
Vega solves the problem you stated:
"PacBio sequencing is typically done by large service centres with large queues and substantial turnaround times, often measured in weeks or months."
Getting a machine in the lab means HiFi data in a day.
Vega solves the problem you stated:
"PacBio sequencing is typically done by large service centres with large queues and substantial turnaround times, often measured in weeks or months."
Getting a machine in the lab means HiFi data in a day.
Cost can be measured in many ways, not just cap-ex and consumables. There is compute time for processing (base calling for some reads is expensive), some reads need post-hoc error correction, etc. If you are paying for HPC resources, that adds up too, even before secondary analysis.
November 4, 2025 at 8:11 PM
Cost can be measured in many ways, not just cap-ex and consumables. There is compute time for processing (base calling for some reads is expensive), some reads need post-hoc error correction, etc. If you are paying for HPC resources, that adds up too, even before secondary analysis.
Fair, but we can agree it's a lot cheaper than Revio and avoids consumables markup from core facilities.
Everyone still needs to choose the right tech based on their resources and goals, which always seem to be changing too.
Everyone still needs to choose the right tech based on their resources and goals, which always seem to be changing too.
November 4, 2025 at 8:07 PM
Fair, but we can agree it's a lot cheaper than Revio and avoids consumables markup from core facilities.
Everyone still needs to choose the right tech based on their resources and goals, which always seem to be changing too.
Everyone still needs to choose the right tech based on their resources and goals, which always seem to be changing too.
David have you heard of the PacBio Vega system? I think you are perpetuating an outdated view, now that the bench-top sequencer is available.
www.pacb.com/vega/
www.pacb.com/vega/
Vega benchtop system - PacBio
The Vega benchtop system - The first HiFi benchtop system - bringing industry-leading and exceptionally accurate long-reads to your lab.
www.pacb.com
November 3, 2025 at 7:25 PM
David have you heard of the PacBio Vega system? I think you are perpetuating an outdated view, now that the bench-top sequencer is available.
www.pacb.com/vega/
www.pacb.com/vega/
Reposted by Dan Portik
Our preprint on our new metagenomic HiFi assembler Alice is out 🥳 Based on a *new sketching method* (🧵1/6)
👉 Preprint www.biorxiv.org/content/10.1...
👉 Github github.com/rolandfaure/...
👉 Preprint www.biorxiv.org/content/10.1...
👉 Github github.com/rolandfaure/...
Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching
We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an assembler that operates directly on these sketches. MSR produces ...
www.biorxiv.org
October 3, 2025 at 2:51 PM
Our preprint on our new metagenomic HiFi assembler Alice is out 🥳 Based on a *new sketching method* (🧵1/6)
👉 Preprint www.biorxiv.org/content/10.1...
👉 Github github.com/rolandfaure/...
👉 Preprint www.biorxiv.org/content/10.1...
👉 Github github.com/rolandfaure/...
Reposted by Dan Portik
Excited to share our LongTrack study out in
@natmicrobiol.nature.com today!
Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/
📄 rdcu.be/eL8mR
@natmicrobiol.nature.com today!
Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/
📄 rdcu.be/eL8mR
Long-read metagenomics for strain tracking after faecal microbiota transplant
Nature Microbiology - A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains...
rdcu.be
October 22, 2025 at 3:39 PM
Excited to share our LongTrack study out in
@natmicrobiol.nature.com today!
Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/
📄 rdcu.be/eL8mR
@natmicrobiol.nature.com today!
Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/
📄 rdcu.be/eL8mR
Another #metagenome assembly algorithm for #PacBio HiFi data - introducing Alice!
I'll be very interested to see how this performs on some of our trickier datasets.
More broadly, I'm happy to see continual development of tools for long-read #metagenomics.
doi.org/10.1101/2025...
I'll be very interested to see how this performs on some of our trickier datasets.
More broadly, I'm happy to see continual development of tools for long-read #metagenomics.
doi.org/10.1101/2025...
Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching
We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an as-sembler that operates directly on these sketches. MSR produces...
doi.org
October 15, 2025 at 4:24 PM
Another #metagenome assembly algorithm for #PacBio HiFi data - introducing Alice!
I'll be very interested to see how this performs on some of our trickier datasets.
More broadly, I'm happy to see continual development of tools for long-read #metagenomics.
doi.org/10.1101/2025...
I'll be very interested to see how this performs on some of our trickier datasets.
More broadly, I'm happy to see continual development of tools for long-read #metagenomics.
doi.org/10.1101/2025...
Reposted by Dan Portik
My new tool Paraviewer is now available for use at github.com/PacificBiosc...! If you use Paraphase, try this new next-step tool - it automates and greatly simplifies variant visualization from Paraphase variant calling. If you're at #ASHG2025, visit me today at poster 4109W. #pacbio
GitHub - PacificBiosciences/Paraviewer
Contribute to PacificBiosciences/Paraviewer development by creating an account on GitHub.
github.com
October 15, 2025 at 2:58 PM
My new tool Paraviewer is now available for use at github.com/PacificBiosc...! If you use Paraphase, try this new next-step tool - it automates and greatly simplifies variant visualization from Paraphase variant calling. If you're at #ASHG2025, visit me today at poster 4109W. #pacbio
Reposted by Dan Portik
#PacBio announces major upcoming advances for #Revio and #Vega designed to lower genome costs, expand multiomic capabilities, and support regulated research.
The SPRQ-Nx chemistry, now in beta access, delivers complete genomes for under $300 at scale.
View the press release: bit.ly/4o06eyH
The SPRQ-Nx chemistry, now in beta access, delivers complete genomes for under $300 at scale.
View the press release: bit.ly/4o06eyH
October 14, 2025 at 3:33 PM
#PacBio announces major upcoming advances for #Revio and #Vega designed to lower genome costs, expand multiomic capabilities, and support regulated research.
The SPRQ-Nx chemistry, now in beta access, delivers complete genomes for under $300 at scale.
View the press release: bit.ly/4o06eyH
The SPRQ-Nx chemistry, now in beta access, delivers complete genomes for under $300 at scale.
View the press release: bit.ly/4o06eyH
Reposted by Dan Portik
omicsomics.blogspot.com/2025/10/pacb... $300 LongRead personal genome via PacBio
PacBio: $300 Genome Via Chemistry Update
ASHG is here in Boston, just down the street from Ginkgo's HQ. I'm in a new role in Ginkgo Automation, trying to convince the NGS world tha...
omicsomics.blogspot.com
October 14, 2025 at 2:35 PM
omicsomics.blogspot.com/2025/10/pacb... $300 LongRead personal genome via PacBio