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
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
Reposted by Dan Portik
#PACB PacBio Announces Major Advances for Revio and Vega to Lower Genome Cost and Expand Multiomic Capabilities
https://www.stocktitan.net/news/PACB/pac-bio-announces-major-advances-for-revio-and-vega-to-lower-genome-ynph3qjnhmeq.html
https://www.stocktitan.net/news/PACB/pac-bio-announces-major-advances-for-revio-and-vega-to-lower-genome-ynph3qjnhmeq.html
PacBio Announces Major Advances for Revio and Vega to Lower Genome Cost and Expand Multiomic Capabilities
PacBio (NASDAQ: PACB), developer of the world's most advanced sequencing technologies, today announced innovations to its Revio and Vega
www.stocktitan.net
October 14, 2025 at 10:05 AM
#PACB PacBio Announces Major Advances for Revio and Vega to Lower Genome Cost and Expand Multiomic Capabilities
https://www.stocktitan.net/news/PACB/pac-bio-announces-major-advances-for-revio-and-vega-to-lower-genome-ynph3qjnhmeq.html
https://www.stocktitan.net/news/PACB/pac-bio-announces-major-advances-for-revio-and-vega-to-lower-genome-ynph3qjnhmeq.html
Reposted by Dan Portik
Reposted by Dan Portik
My complex variant visualization tool SVTopo is now officially published in BMC Genomics! link.springer.com/article/10.1.... This tool allows HiFi users to view complex germline structural variation in intuitive and informative plots.
Complex structural variant visualization with SVTopo - BMC Genomics
Background Structural variants are genomic variants that impact at least 50 nucleotides. Structural variants can play major roles in diversity and human health. Many structural variants are difficult to interpret and understand with existing visualization tools, especially when comprised of inverted sequences or multiple breakend pairs. Results We present SVTopo, a tool to visualize germline structural variants with supporting evidence from high-accuracy long reads in easily understood figures. We include examples of 101 visually complex structural variants from seven unrelated human genomes, manually assigned to ten categories. These demonstrate a broad spectrum of rearrangement and showcase the frequency of complex structural variants in human genomes. Conclusions SVTopo shows breakpoint evidence in ways that aid reasoning about the impact of multi-breakpoint rearrangements. The images created aid human reasoning about the result of structural variation on gene and regulatory regions.
link.springer.com
October 9, 2025 at 7:00 PM
My complex variant visualization tool SVTopo is now officially published in BMC Genomics! link.springer.com/article/10.1.... This tool allows HiFi users to view complex germline structural variation in intuitive and informative plots.
Reposted by Dan Portik
I'm excited to share our pre-print about a new variant benchmarking tool we've been working on for the past few months!
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
October 6, 2025 at 8:07 PM
I'm excited to share our pre-print about a new variant benchmarking tool we've been working on for the past few months!
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
Reposted by Dan Portik
Most plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social
Megaplasmids associate with Escherichia coli and other Enterobacteriaceae https://www.biorxiv.org/content/10.1101/2025.09.30.679422v1
October 1, 2025 at 5:10 AM
Most plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social
New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut.
Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals.
doi.org/10.1101/2025...
Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals.
doi.org/10.1101/2025...
Megaplasmids associate with Escherichia coli and other Enterobacteriaceae
Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...
doi.org
October 1, 2025 at 4:44 PM
New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut.
Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals.
doi.org/10.1101/2025...
Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals.
doi.org/10.1101/2025...
Reposted by Dan Portik
Metagenomics for Microbiology 2nd Ed provides an opportunity to reflect on the growth of the metagenomics field, from new applications to technological advances. The chapters cover methodology, analysis, AI, omics, and more.
shop.elsevier.com/books/metage...
#microbiome #omics #DataScience
shop.elsevier.com/books/metage...
#microbiome #omics #DataScience
Metagenomics for Microbiology
Metagenomics for Microbiology, Second Edition unveils the intricate and diverse world of microbial communities, emphasizing their critical roles in he
shop.elsevier.com
September 28, 2025 at 9:49 PM
Metagenomics for Microbiology 2nd Ed provides an opportunity to reflect on the growth of the metagenomics field, from new applications to technological advances. The chapters cover methodology, analysis, AI, omics, and more.
shop.elsevier.com/books/metage...
#microbiome #omics #DataScience
shop.elsevier.com/books/metage...
#microbiome #omics #DataScience
Reposted by Dan Portik
Long and Kelsey just won the 2025 Microbiome SMRT Grant for HiFi shotgun metagenomics!! They will collaborate to optimize PacBio-compatible protocols for gut metagenomics, specifically generating high quality long-read data from IBD patients. Congrats to both! 🎉 🎉 www.pacb.com/blog/2025-mi...
September 17, 2025 at 6:58 PM
Long and Kelsey just won the 2025 Microbiome SMRT Grant for HiFi shotgun metagenomics!! They will collaborate to optimize PacBio-compatible protocols for gut metagenomics, specifically generating high quality long-read data from IBD patients. Congrats to both! 🎉 🎉 www.pacb.com/blog/2025-mi...
Reposted by Dan Portik
@dportik.bsky.social and I wrote a book chapter on highly accurate #longread @pacbio.bsky.social HiFi sequencing for #microbiome and #metagenomic applications in "Metagenomics for Microbiology (Second Edition)" that is now published! Check it out here:
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
www.sciencedirect.com
August 18, 2025 at 3:15 PM
@dportik.bsky.social and I wrote a book chapter on highly accurate #longread @pacbio.bsky.social HiFi sequencing for #microbiome and #metagenomic applications in "Metagenomics for Microbiology (Second Edition)" that is now published! Check it out here:
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Dan Portik
The human #microbiome holds enormous potential, but only if we can see it clearly.
Join this webinar to learn how #PacBio HiFi sequencing delivers accurate, high-resolution insights with 16S rRNA sequencing and shotgun metagenomics.
Secure your spot: bit.ly/4mYmK1G
Join this webinar to learn how #PacBio HiFi sequencing delivers accurate, high-resolution insights with 16S rRNA sequencing and shotgun metagenomics.
Secure your spot: bit.ly/4mYmK1G
September 8, 2025 at 7:34 PM
The human #microbiome holds enormous potential, but only if we can see it clearly.
Join this webinar to learn how #PacBio HiFi sequencing delivers accurate, high-resolution insights with 16S rRNA sequencing and shotgun metagenomics.
Secure your spot: bit.ly/4mYmK1G
Join this webinar to learn how #PacBio HiFi sequencing delivers accurate, high-resolution insights with 16S rRNA sequencing and shotgun metagenomics.
Secure your spot: bit.ly/4mYmK1G
This could be a neat method for species detection in #metagenomic datasets, but why on earth are we simulating PacBio and ONT error rates at >10%? 🫣🤔🫠
PacBio HiFi has had >99% accuracy since 2019.
Very hard to interpret the results based on 90% accuracy.
www.biorxiv.org/content/10.1...
PacBio HiFi has had >99% accuracy since 2019.
Very hard to interpret the results based on 90% accuracy.
www.biorxiv.org/content/10.1...
TIPP-SD: A New Method for Species Detection in Microbiomes
In this study, we present TIPP-SD (i.e., TIPP for Species Detection), a new technique for species detection in a microbiome sample. TIPP-SD uses a modified version of TIPP3, which is a recently develo...
www.biorxiv.org
September 10, 2025 at 4:18 PM
This could be a neat method for species detection in #metagenomic datasets, but why on earth are we simulating PacBio and ONT error rates at >10%? 🫣🤔🫠
PacBio HiFi has had >99% accuracy since 2019.
Very hard to interpret the results based on 90% accuracy.
www.biorxiv.org/content/10.1...
PacBio HiFi has had >99% accuracy since 2019.
Very hard to interpret the results based on 90% accuracy.
www.biorxiv.org/content/10.1...
New #metagenome assembly comparison of PacBio, ONT, and Illumina in human gut #microbiomes.
- "HiFi generated more cMAGs than ONT at every depth with either assembly method"
- "HiFi cMAGs had significantly higher completeness and lower contamination than ONT"
doi.org/10.1016/j.ce...
- "HiFi generated more cMAGs than ONT at every depth with either assembly method"
- "HiFi cMAGs had significantly higher completeness and lower contamination than ONT"
doi.org/10.1016/j.ce...
Redirecting
doi.org
September 10, 2025 at 3:57 PM
New #metagenome assembly comparison of PacBio, ONT, and Illumina in human gut #microbiomes.
- "HiFi generated more cMAGs than ONT at every depth with either assembly method"
- "HiFi cMAGs had significantly higher completeness and lower contamination than ONT"
doi.org/10.1016/j.ce...
- "HiFi generated more cMAGs than ONT at every depth with either assembly method"
- "HiFi cMAGs had significantly higher completeness and lower contamination than ONT"
doi.org/10.1016/j.ce...
Reposted by Dan Portik
This PacBio lego puzzle was fun! But lorrrrrrdddyyyyy the instructions 🙈🙈🙈
June 24, 2025 at 11:57 PM
This PacBio lego puzzle was fun! But lorrrrrrdddyyyyy the instructions 🙈🙈🙈
Reposted by Dan Portik
Reposted by Dan Portik
Checking out @pacbio.bsky.social at #ASMicrobe!
June 21, 2025 at 9:43 PM
Checking out @pacbio.bsky.social at #ASMicrobe!
Very excited to see the long-read #microbiome profiling feature included in this tool! I'll be taking a look at #PacBio HiFi performance in the near future.
The new version of MetaPhlAn v4.2.2 released!
📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs
Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...
📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs
Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...
MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update)
Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhl...
forum.biobakery.org
June 11, 2025 at 7:30 PM
Very excited to see the long-read #microbiome profiling feature included in this tool! I'll be taking a look at #PacBio HiFi performance in the near future.
Reposted by Dan Portik
Mapler: A pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads. #Metagenomics #HiFi #LongReads #Sequencing #GenomeAssembly #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
June 11, 2025 at 9:15 AM
Mapler: A pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads. #Metagenomics #HiFi #LongReads #Sequencing #GenomeAssembly #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Reposted by Dan Portik
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
myloasm-docs.github.io
myloasm - metagenomic assembly with (noisy) long reads
myloasm-docs.github.io
May 28, 2025 at 5:54 PM
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
myloasm-docs.github.io