Ryan Doughty

I had the privilege of working on one of the tools studied here, SeqScreen. SeqScreen was part of this evaluation where every tool hit >95% sensitivity and >97% accuracy; disagreements were mostly isolated and tied to SOC definition differences.

bronko: ultrafast, alignment-free detection of viral genome variation As viral sequencing datasets continue to grow, traditional alignment-based variant calling pipelines are becoming computationally prohibitive. To address these challenges, we developed bronko , an ult...

Here is the link to the preprint:

www.biorxiv.org/content/10.6...

GitHub - treangenlab/bronko: Ultra-rapid detection of viral variants directly from sequencing data Ultra-rapid detection of viral variants directly from sequencing data - treangenlab/bronko

Give it a try and let us know what you think. As with any project, any feedback/thoughts from the community are well appreciated! Written in Rust :)
github.com/treangenlab/...

6/n

For samples that are aligned to a single reference, bronko can also generate a multiple sequence alignment, which can be directly input into downstream phylogenetic/transmission inference tools. We found that the SNPs identified matched well with Parsnp2 in cases of low divergence.

5/n

bronko also take multiple samples and multiple references, mapping each sample against all of the references at once. This allows us to choose the reference that most closely matches the reference genome, reducing biases that can arise from distant references

4/n

To achieve this, we utilized a (1,2) locality-sensitive bucketing function, which matches kmers with <= 1 edit distance from the reference and precisely identifies SNPs/iSNVs within those kmers. Combined with a pseudomapping approach, we can identify most variants directly from k-mer counts.

3/n

bronko method overview

We developed bronko, an alignment-free approach that bypasses both read-alignment + variant calling and provides variant calls (SNPs and iSNVs) directly from sequencing reads and a reference genome (or set of reference genomes), enabling viral genome analyses across petabyte-scale databases

2/n

Some of my work from the first year of my PhD is out as a preprint, please check it out!

Virus evolution is rapid and prolific both across and within individuals. However, a significant amount of variation remains hidden due to computational bottlenecks in read-alignment and variant calling

1/n

A Comparison of Methods for the Optimal Recovery of the Human Fecal Virome https://www.medrxiv.org/content/10.1101/2025.05.12.25327428v1

Upcoming wastewater virome webinar from Dr. Mike Tisza, Feb. 12! Free for everyone.
More: coms.osu.edu/events/early...

#virus #virome #viromics #pathogen #sequencing #microbiome #microbe #bacteria #science #microbiology #webinar

Longitudinal phage–bacteria dynamics in the early life gut microbiome - Nature Microbiology Reanalysis of 12,262 longitudinal infant gut microbiome samples using the Marker-MAGu pipeline revealed phage–bacteria dynamics over the first year of life.

We interrupt your regularly-scheduled chaos to bring you some cool microbiome science. 🦠 🖥️ 🧬
"Longitudinal phage–bacteria dynamics in the early life gut microbiome" now out in Nature Microbiology.

We wanted a way to measure bacteria and phage in metagenomes 1/

www.nature.com/articles/s41...

Congrats to Bryce Kille on absolutely smashing his PhD defense at Rice today with advisor @treangen.bsky.social ! Collaborating with Bryce over the past few years has been an absolute delight 👏🎉👏🎉