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
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.
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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:
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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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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.
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And some summaries by several #genomics folks:. Keith Robison (@OmicsOmicsBlog):. Nava Whiteford:. Shawn Baker (@SanDiegOmics):.
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It's beautiful weather today at the #cshlmbiome conference! . @PacBio just hosted a packed microbial workshop featuring guest speaker @gangfang_1. He talked about studying the stable and dynamic nature of bacterial epigenomes, with an emphasis on HiFi #methylation data.
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Also, I consider many things beyond performance when deciding whether or not to include a tool in a workflow: .- ease of installation.- active tool maintenance .- resource requirements.- reliance on databases.Just to name a few!.
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A new #metagenomic binning algorithm has appeared: TaxVAMB. Looks like it may outperform SemiBin2 for @PacBio HiFi datasets (human gut). I use the long-read mode of SemiBin2 in the HiFi-MAG-Pipeline and it works great. Time to run some benchmarks!.
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