Daniel Portik
@DPortik
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Bioinformatics scientist @PacBio. I work on metagenomics, methylation, and assembly, but also enjoy phylogenomics and frog/lizard evolution. 🦠 🐸 🦎 🧬
Joined February 2021
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. Happy to see continual development of tools for long-read #metagenomics. https://t.co/SXMLHvhlVk
biorxiv.org
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...
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Complex structural variant visualization with SVTopo. #GeneticVariants #StructuralVariants #VariantsVisualization #BMCgenomics
https://t.co/VnTpRoiWBS
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PacBio: $300 Genome Via Chemistry Update 🧬🖥️ https://t.co/ujDfFbAofl
#ASHG2025
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New Banfield lab pre-print highlighting 1.5Mb megaplasmids found in human gut. #Plasmid genomes were resolved using @PacBio HiFi sequencing and hifiasm-meta for #metagenome assembly. Host association was detected using #epigenetic signals. https://t.co/6kqHFN6aCx
biorxiv.org
Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae...
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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 accuracy is >99% since 2019. Very hard to interpret the results based on 90% accuracy. https://t.co/N49YL28esy
biorxiv.org
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...
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New #metagenome assembly comparison of PacBio, ONT, and Illumina in 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" https://t.co/1BCNZd5qfC
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Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler. With @lh3lh3. https://t.co/ingqEXblza
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Great keynote talk at #SFAF by Rob Knight, summarizing key innovations in #microbiome research over the past decade. One recent highlight is how long reads have transformed #metagenome assembly, particularly @PacBio HiFi reads. The future is complete MAGs!
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Do you think long-read #metagenomics with #PacBio #HiFi is gaining momentum? I noticed there were more publications & pre-prints on this topic in 2024 (56) than 2022 + 2023 combined (54). Definitely encouraging! Full pub list: https://t.co/1joAk1RwTp
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#Fire in San Diego in Linda Vista/Fashion Valley area, now called #Friar Fire. I took this video from our apartment complex and hope this helps with the effort to extinguish it quickly. We evacuated minutes after I recorded this. @nbcsandiego
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A bright new day is here! 🦋 Follow us on Bluesky ( https://t.co/UZ52dV9svz) and stay connected for updates, innovations, and everything genomics. #PacBio
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Another very insightful paper on #methylation and long-read sequencing by @gangfang_1, describing some important but frequently overlooked caveats. Gang provides a fantastic summary in his post, but here's my take too😅:
Preprint alert 🚨 Cautions in the use of @nanopore sequencing to map DNA modifications: officially reported “accuracy” ≠ reliable mapping in real applications. We performed a critical assessment of nanopore sequencing (across different versions of models) for the detection of
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lol - I wasn't going to say it 😅
Desperate.
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BGC yields look great for human gut, chicken gut, sludge, and sheep gut, with many complete BGCs recovered! There might also be room for future improvement - the authors report ~70% of run time is antiSMASH. TLDR: BGCs are easy with @PacBio HiFi metagenome assembly.
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Interesting work on biosynthetic gene clusters (BGCs) with @PacBio HiFi #metagenomic datasets. HiFiBGC assembles contigs using three methods, runs antiSMASH on the contigs and unassembled reads, and de-replicates resulting BGCs through clustering. https://t.co/nT5HFRFScS
bmcgenomics.biomedcentral.com
Background Microbes produce diverse bioactive natural products with applications in fields such as medicine and agriculture. In their genomes, these natural products are encoded by physically...
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And some summaries by several #genomics folks: Keith Robison (@OmicsOmicsBlog): https://t.co/986pMmKAAs Nava Whiteford: https://t.co/uxxdzPznwF Shawn Baker (@SanDiegOmics): https://t.co/dwQCnE3Xcz
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The full spec sheet with more details is available here: https://t.co/DXHp7gL7BK
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It's official, @PacBio has launched a new benchtop sequencer! Quick summary of the new Vega system: - instrument = $169k - consumables = $1100 per run - output = 60 Gbp, 24 hr run time This is the #HiFi sequencer #microbiology labs have been asking for. https://t.co/RYJdUCq8SA
pacb.com
Priced at just $169,000 Vega is designed to make highly accurate long-read sequencing accessible to any laboratory Translations: Japanese | Chinese | Korean MENLO PARK, Calif., Nov. 06, 2024...
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If #ASHG attendees can count on one thing lately, it’s @PacBio creating a buzz (and throwing a great party). This year was no exception! When PacBio launched their latest instrument, Vega, on Wednesday night, @OneRepublic was on site to help them do it. https://t.co/QXzw586AOk
genengnews.com
PacBio launches the Vega System: a new sequencing platform that brings the company's HiFi sequencing technology to the benchtop.
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