For anyone doing ONT Microbial Genomics, please take 1 minute (less?) to tell us which assembly metrics you care most about when evaluating whether an assembly is "good". We are doing a benchmark of different QC tools (barcode/adapter trimming and QC filtering). microbial-qc-survey.streamlit.app

Microbial QC Survey

A standalone Streamlit app that collects community priority weights over fourassembly-QC metrics ...

microbial-qc-survey.streamlit.app

Rapid diagnosis of common, undetected, and uncultivable bloodstream infections from positive blood cultures using Oxford Nanopore sequencing: a metagenomic pipeline analysis - The Lancet Microbe www.thelancet.com/journals/lan... #microsky

Rapid diagnosis of common, undetected, and uncultivable bloodstream infections from positive blood cultures using Oxford Nanopore sequencing: a metagenomic pipeline analysis

These findings show that metagenomic sequencing has the potential to rapidly and comprehensively detect pathogens and AMR in bloodstream infections. Integration into clinical practice could help to cl...

thelancet.com

Come to ONT's industry event at ASM to hear about two exciting new tools from @jimshaw.bsky.social! SNPmers (polymorphic kmers) are leveraged for impressive performance in both myloasm (metagenomic assembly) and savont (16S ASVs). Registration link 👇

Oxford Nanopore@nanoporetech.com · 2mo ago

Join Jim Shaw at #ASMicrobe to uncover how to unlock high-resolution, strain-level microbiome insights. Learn how this is could be crucial to helping deliver more precise diagnostics and treatment in the future. https://bit.ly/4v4XuKE

Note that I released a new version of metaMDBG (v1.4) last week focusing on scalability. You can now process such dataset in 6 days and 130 GB of memory

Christine He@christinehe.bsky.social · 3mo ago

Released today: ~1.5 Tbp of ONT metagenomic sequencing from compost. Assembly, MAGs, and downstream analysis are available to play with epi2me.nanoporetech.com/compost_mgx_...

Released today: ~1.5 Tbp of ONT metagenomic sequencing from compost. Assembly, MAGs, and downstream analysis are available to play with epi2me.nanoporetech.com/compost_mgx_...

Metagenomic Assembly Sheds Light on Microbial Diversity in Compost

Overview We are pleased to release a metagenomic dataset from deep sequencing of a mature compost…

epi2me.nanoporetech.com

ONT has a temporary bioinformatics position (8 months) open while I'm on maternity leave. Focus will be on microbial genomics but with opportunities to work on projects across the breadth of genomics! ejnh.fa.em2.oraclecloud.com/hcmUI/Candid...

An ONT webinar where I discuss wet and dry lab methods for environmental metagenomics, as well as analysis of 1.5 Tb (!!) of metagenomic sequencing from compost. Featuring the nanoMDBG assembler, strain-dependent AMR profiles, and invertons: www.youtube.com/watch?v=OZ4P...

Exploring Oxford Nanopore sequencing methods for environmental samples

YouTube video by Oxford Nanopore Technologies

youtube.com

Our guide for best practices in metagenomic assembly and binning of @nanoporetech.com data, highlighting some exciting recently developed tools for high accuracy long reads

Sean McKenzie@dorylophile.bsky.social · 2y ago

Check out our new Apps Note on metagenomic assembly of the Zymo fecal reference with nanopore sequencing and metaMDBG. Almost 200 Gb of metagenomic sequence data from a single PromethION flowcell, yeilding hundreds of high-quality metagenome assembled genomes: nanoporetech.com/resource-cen...

NCBI's Taxonomy changes over time. We built Taxonomy Time Machine to track these changes: 🕰️ app: taxonomy.onecodex.com 📄 pre-print: www.biorxiv.org/content/10.1...