Lightnews — Scholar-powered news

Reposted by Dan Portik

Matt Holt @holtjma.bsky.social · 1d

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

1 16 29

Reposted by Dan Portik

Allison G @assemblerag.bsky.social · 7d

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

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 7d

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae https://www.biorxiv.org/content/10.1101/2025.09.30.679422v1

2 16 28

Dan Portik @dportik.bsky.social · 6d

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...

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

1 22 48

Reposted by Dan Portik

Jacques Izard @jacquesizard.bsky.social · 9d

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

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

2 6

Reposted by Dan Portik

Hutlab @hutlab.bsky.social · 20d

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...

1 4 10

Reposted by Dan Portik

Jeremy Wilkinson @jewilki.bsky.social · Aug 18

@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

2 2

Dan Portik @dportik.bsky.social · 21d

Awesome! Check out the methods here which are focused on HiFi metagenome assembly in a pooled human gut microbiome:
www.biorxiv.org/content/10.1...

I strongly recommend using hifiasm-meta, and potentially metaMDBG as well. Also, make sure you use the proper tools for binning long-reads assemblies.

Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods

Long-read metagenomic sequencing is a powerful approach for cataloging the microbial diversity present in complex microbiomes, including the human gut microbiome. We performed a deep-sequencing experi...

www.biorxiv.org

2

Reposted by Dan Portik

PacBio @pacbio.bsky.social · 29d

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

4 6

Dan Portik @dportik.bsky.social · 27d

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...

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

1 1 1

Dan Portik @dportik.bsky.social · 27d

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...

Redirecting

doi.org

1 5 9

Reposted by Dan Portik

Elinne Becket, PhD @bielleogy.bsky.social · Jun 24

This PacBio lego puzzle was fun! But lorrrrrrdddyyyyy the instructions 🙈🙈🙈

2 2 17

Reposted by Dan Portik

Jonathan Jacobs @bioinformer.bsky.social · Jun 22

#ASMicrobe ❤️ LA // @tallcuppajoe.bsky.social @bielleogy.bsky.social @gfahurbottino.bsky.social @jlgoff.bsky.social @lebetimonas.bsky.social @dportik.bsky.social @jcamthrash.bsky.social @ahoiching.bsky.social @germjuggler.bsky.social @scottnguyen.bsky.social

1 6 23

Reposted by Dan Portik

Binning Singletons @binningsingletons.com · Jun 21

Checking out @pacbio.bsky.social at #ASMicrobe!

2 5

Dan Portik @dportik.bsky.social · Jun 11

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.

Segata Lab @cibiocm.bsky.social · Jun 11

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-...

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

3 5

Reposted by Dan Portik

Javier Santoyo @jsantoyo.bsky.social · Jun 11

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...

1 5

Reposted by Dan Portik

Jim Shaw @jimshaw.bsky.social · May 28

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 - metagenomic assembly with (noisy) long reads

myloasm-docs.github.io

5 78 130

Dan Portik @dportik.bsky.social · May 22

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!

1 3 10

Dan Portik @dportik.bsky.social · May 7

Would also love to see how many terabases of sequencing to get to 95% mapping!

1 3

Dan Portik @dportik.bsky.social · May 7

Here is an example from a lake water column microbiome, sequenced with #PacBio HiFi. In the HiFi-MAG-Pipeline, I look at reads mapped to all contigs, all bins (passing or failing QC), and only bins that pass QC (e.g., MAGs). The numbers vary by sample, but the overall pattern holds.

4

Dan Portik @dportik.bsky.social · Apr 22

Another great tool from the Computational Biology group at #PacBio. This one helps visualize complex structural variants detected using long reads.

Congrats to @jonbelyeu.bsky.social and the rest of the team!

Jon Belyeu @jonbelyeu.bsky.social · Apr 22

I just released a new preprint! The manuscript describes SVTopo, a software tool that enhances visualization of complex SVs using HiFi data: www.biorxiv.org/content/10.1.... Here’s a summary of the results:

Complex structural variant visualization with SVTopo

Structural variants are genomic variants that impact at least 50 nucleotides and can play major roles in diversity and human health. Many structural variants are complex multi-breakpoint rearrangement...

www.biorxiv.org

3

Dan Portik @dportik.bsky.social · Apr 10

Another great #HiFi tool produced by the CompBio group at #PacBio. This one is a big leap forward for structural variants, particularly for long-read sequencing.

Congrats to @ctsa.bsky.social and others!

Chris Saunders @ctsa.bsky.social · Apr 10

Great to see that sawfish, our new HiFi SV caller, is accepted for publication in Bioinformatics! Sawfish emphasizes local haplotype modeling to improve SV representation and genotyping in both single and joint-sample analysis. Advance-access article now available: (1/n)

doi.org/10.1093/bioi...

Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling

AbstractMotivation. Structural variants (SVs) play an important role in evolutionary and functional genomics but are challenging to characterize. High-accu

doi.org

2 7

Reposted by Dan Portik

PacBio @pacbio.bsky.social · Apr 9

The University of Bern (@bernomics.bsky.social) is taking sequencing to the next level with #SPRQ chemistry on #Revio. Increased data yield and better quality across diverse samples, like naked mole rats, show how HiFi is changing the game.

Blog here: bit.ly/4j5qIDJ

#PacBio #PacBioSPRQ

2 6

Dan Portik @dportik.bsky.social · Mar 28

Interesting pre-print looking at shallow shotgun #metagenomics with short reads for #metagenome profiling, assembly, and function. Pretty clear limitations, but assembly was particularly bad.

Long reads have advantages in all three areas; similar benchmarking approaches would prove useful here.

Cameron Thrash @jcamthrash.bsky.social · Mar 28

Benchmarking of shotgun sequencing depth highlights strain-level limitations of metagenomic analysis www.biorxiv.org/content/10.1... #jcampubs

2 8

Reposted by Dan Portik

Guillaume Méric @gmeric.bsky.social · Feb 25

Nice to see good methods being developped for long-reads metagenomic sequencing analyses. This one focuses on attempting to use coverage of long reads to assign AMR genes to host microbial species, something that's pretty hard to do with Illumina atm. Looks promising!
www.nature.com/articles/s41...

Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo - Nature Communications

In this study, the authors present ‘Argo’, a bioinformatics tool for identifying the host species for antibiotic resistance genes in long-read metagenomic sequence data. They validate the tool using s...

www.nature.com

7 28

Dan Portik @dportik.bsky.social · Jan 31

Great work! Just out of curiosity, which assembler do you think worked best for the PacBio isolate sequencing?

1