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#sequencing

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naturepoker

1 of 2 posters for the summer picked up! I'll be presenting this one at upcoming Boston Bacterial Meeting #BBM2025.

A specific type of plasmid replication gene (RPA) is overreprented among Deinococcota & analysis hints at introduction of the MGE early in its history, tracing back to Allomeiothermus #microbiology #amateurbiology #sequencing

Since this is polishing up of such an older data, I'd say it's the most amateur-like (in a good way) of all stuff coming out of our warehouse lab right now

naturepoker

What do #nanopore #sequencing #bioinformatics folks think about this one? New preprint on hashing raw nanopore signals and using them directly for de-novo assembly.

arxiv.org/abs/2503.02997v1

Hypothetical blow5-to-assembly pipe would be interesting, though figuring it out is way out of my depth.

arXiv.orgEnabling Fast, Accurate, and Efficient Real-Time Genome Analysis via New Algorithms and TechniquesThe advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data present significant challenges related to accuracy, scalability, and computational efficiency. These challenges are mainly due to various forms of unwanted and unhandled variations in sequencing data, collectively referred to as noise. In this dissertation, we address these challenges by providing a deep understanding of different types of noise in genomic data and developing techniques to mitigate the impact of noise on genome analysis. First, we introduce BLEND, a noise-tolerant hashing mechanism that quickly identifies both exactly matching and highly similar sequences with arbitrary differences using a single lookup of their hash values. Second, to enable scalable and accurate analysis of noisy raw nanopore signals, we propose RawHash, a novel mechanism that effectively reduces noise in raw nanopore signals and enables accurate, real-time analysis by proposing the first hash-based similarity search technique for raw nanopore signals. Third, we extend the capabilities of RawHash with RawHash2, an improved mechanism that 1) provides a better understanding of noise in raw nanopore signals to reduce it more effectively and 2) improves the robustness of mapping decisions. Fourth, we explore the broader implications and new applications of raw nanopore signal analysis by introducing Rawsamble, the first mechanism for all-vs-all overlapping of raw signals using hash-based search. Rawsamble enables the construction of de novo assemblies directly from raw signals without basecalling, which opens up new directions and uses for raw nanopore signal analysis.
naturepoker

For sequencing curious folks: a lab is trying to use up their last NextSeq 550 flowcell, and they're willing to run it for anyone for cost of the flowcell or less (likely a lot less).

Anyone interested in 30~39Gb worth of 150bp reads, let me know! We have about a week to figure this out.

Amateurs and independent researchers welcome too, but you'll have to extract your own DNA and send it to us.

#bioinformatics#sequencing#microbiology
Replied in thread
SatinBrooch

@firefoxx66 People who are interested in that, might also be interested in:
* the GenomeTrakr Network fda.gov/food/whole-genome-sequ
* GCpathogen (potentially) nmdc.cn/gcpathogen/ ( ncbi.nlm.nih.gov/pmc/articles/ )

Open Sourcing databases with a sharp focus like that are essential for good research. Especially if there is a good interoperability and thus data exchange which seems to be the case with pathoplexus.

U.S. Food and Drug Administration · GenomeTrakr NetworkThe GenomeTrakr network is the first distributed network of laboratories to utilize whole genome sequencing for pathogen identification.
#sequencing#research#opendata
Nigel

Well, have decided to try my hand at creating music with #sequencing after rekindling my interest in #electronicmusic - bearing in mind the last time I used a sequencer it was an #Alesis MMT8 - and it was new!

This time it will all be #inthebox though. Cubase includes a simple but handy sequencer called Step Designer and I've installed the free VST plugin called #Stochas which has more advanced capabilities like 'probability' attribute per note and more... I may be 'asking the audience'.. soon!

Giuseppe Michieli

#Virome #Sequencing Identifies #H5N1 Avian #Influenza in #Wastewater from Nine #Cities. MedRxIV, medrxiv.org/content/10.1101/20

19 of 23 monitored sites had at least one detection event, and H5N1 serotype became dominant over seasonal influenza over time. A variant analysis suggests avian or #bovine origin but other potential sources, especially humans, could not be excluded.

medRxiv · Virome Sequencing Identifies H5N1 Avian Influenza in Wastewater from Nine Cities.Avian influenza (serotype H5N1) is a highly pathogenic virus that emerged in domestic waterfowl in 1996. Over the past decade, zoonotic transmission to mammals, including humans, has been reported. Although human to human transmission is rare, infection has been fatal in nearly half of patients who have contracted the virus in past outbreaks. The increasing presence of the virus in domesticated animals raises substantial concerns that viral adaptation to immunologically naive humans may result in the next flu pandemic. Wastewater-based epidemiology (WBE) to track viruses was historically used to track polio and has recently been implemented for SARS-CoV2 monitoring during the COVID-19 pandemic. Here, using an agnostic, hybrid-capture sequencing approach, we report the detection of H5N1 in wastewater in nine Texas cities, with a total catchment area population in the millions, over a two-month period from March 4th to April 25th, 2024. Sequencing reads uniquely aligning to H5N1 covered all eight genome segments, with best alignments to clade 2.3.4.4b. Notably, 19 of 23 monitored sites had at least one detection event, and the H5N1 serotype became dominant over seasonal influenza over time. A variant analysis suggests avian or bovine origin but other potential sources, especially humans, could not be excluded. We report the value of wastewater sequencing to track avian influenza. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by S.B. 1780, 87th Legislature, 2021 Reg. Sess. (Texas 2021) (E.B., A.W.M., and J.F.P.), NIH/NIAID (Grant number U19 AI44297) (A.W.M.), Baylor College of Medicine Melnick Seed (A.W.M) and Alkek Foundation Seed (J.F.P.), and Pandemic Threat Technology Center (P.A.P.). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced are available online at https://zenodo.org/doi/10.5281/zenodo.11175923 and NCBI SRA BioProject: PRJNA966185
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Lukas VFN 🇪🇺

With only the pawprints, researchers study elusive bobcat phys.org/news/2024-01-pawprint

A novel eDNA approach for rare species monitoring: Application of long-read shotgun #sequencing to #Lynx rufus soil pawprints sciencedirect.com/science/arti by Samantha Koda et al.

"#DNA recovered from #bobcat #pawprints can be used to determine the #animals' ancestral background and even identify their unique #microbial community. All from the errant DNA left behind long after the #animal has left the area."

Lukas VFN 🇪🇺

Using #DNAsequencing to show how marine worms adapt to #DeepSea conditions phys.org/news/2023-10-dna-sequ

Third-Generation #Sequencing Reveals the Adaptive Role of the #Epigenome in Three Deep-Sea #Polychaetes: Maeva Perez et al. academic.oup.com/mbe/article/4

"#epigenetic regulation by #DNAmethylation could be an adaptive mechanism that counteracts the effects of hydrostatic pressure at the bottom of the #ocean"

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Lukas VFN 🇪🇺

Using #DNAsequencing to show how marine #worms adapt to deep-sea conditions phys.org/news/2023-10-dna-sequ

Third-Generation #Sequencing Reveals the Adaptive Role of the #Epigenome in Three #DeepSea #Polychaetes: Maeva Perez et al. academic.oup.com/mbe/article/4

"#Methylation is an #epigenetic process that chemically modifies some of DNA bases. It plays a role in environmental acclimatization, making organisms living in habitats where conditions are unpredictable more resilient to environmental changes"

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