Thanh Le Viet

Excited to discover that two of my software tools (Shovill & Snippy) were used to assemble the genome of the #Hantavirus Andes Chile-9717869 strain. #bioinforbioinformatics #genomics #microbiology

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin and supervised by Heng Li @lh3lh3

Extracting @NCBI SRA files with fasterq-dump can require 17x the size of the accession while decompressing. Our new tool xsra extracts sequences at 5x throughput with significantly less disk usage, built-in compression, and optional BINSEQ outputs github.com/arcInstitute/x…

@flashton2003 Congrats Phil, will you be based in Oxford?

Chuffed to announce that I've started a new job with @daanensen at @TheCGPS in Oxford, supporting the uptake of genomics for AMR in global health!

🦘✂️ Thanks to @cziscience, @wytamma and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again! forms.gle/YJP6WQjsk8KKQx…

⏰ Closing soon! We’re looking for an enthusiastic and motivated Bioinformatics Programmer to join our Core Bioinformatics team. 💷 £43,550 to £54,900 🗓️ Apply by 2 July 2024 ➡️ buff.ly/3VlKEZH

It's time to donate #usearch to the scientific community, with many sincere thanks to users who supported this research through license fees.

Seq data of varying quality can be used for different public health applications (analysis, training, more). @pha4ge standardized QC tags help users share, triage, and identify a wider array of data in public repos. For more info, see: shorturl.at/1yaCw hot off the presses!

@Clarika84 @Ellie__Jameson @gemma_langridge @EvelienAdri @ma_webber Congrats 🎉

Dr >>> Ms Thank you so much for a great experience @Ellie__Jameson and @gemma_langridge. Thanks so much to my supervisors @EvelienAdri and @ma_webber, as well as everyone in the Adriaenssens Group, past and present! #PhDone #PhD

🆕 Vacancy! We’re looking for an enthusiastic and motivated Bioinformatics Programmer to join our Core Bioinformatics team. 💷 £43,550 to £54,900 🗓️ Apply by 2 July 2024 ➡️ buff.ly/3R5y0LO

We have released some raw @nanopore data for benchmarking purposes, along with some basecalled outputs. We use the subset of 20k or 500k for benchmarking tools and methods a LOT! We thought they would be helpful to others too. 4/5kHz R10.4.1 & RNA004 gentechgp.github.io/gtgseq/

Bactopia now supports AllTheBacteria assemblies! 🎉 If you are planning secondary analyses, this feature allows you to seamlessly use Bactopia. To demonstrate this, here's a blog post using Bactopia to analyze 5400 L. pneumophila assemblies bactopia.github.io/latest/blog/20…

🔬 Excited to share the preprint of our latest #research on the genomic diversity & amr in hospital-associated Klebsiella pneumoniae in Southern Ghana 🧬🏥 biorxiv.org/content/10.110… #AMR #genomics 🧵(1/9) @OdarkorMills @humphrey_addy @tweakyaustin @thanhleviet @GSequencing

The fastest way to get your issue fixed in a project is to write a high quality bug report with reproduction and research into solutions. Here is an example of an A+++ issue I received a couple days ago. Complex, but resolved in a few hours because the report was so fantastic. If this person just reported "DPI not handled correctly", this issue probably would've taken weeks or months to resolve considering the back and forth required. The bonus thing is that this issue actually has a mediocre reproduction scenario (since it depends so heavily on external configurations). The description of the issue and research into solutions is so good that I felt comfortable inspecting the change, verifying it didn't break my test systems, and merging it based on the research alone.

Dorado v0.5 NCM release 🎉 - new simplex models - faster - higher accuracy - easier to use (auto model selection) - hemi-methylation (duplex mods) - primer & adapter trimming - custom barcodes #nanoporeconf github.com/nanoporetech/d…

Thrilled to share the first preprint from my lab! We losslessly compressed FM-index using a novel technique called run-block compressed BWT (RBBWT). Building upon it, we implemented the Centrifuger method for taxonomic classification on sequencing data. biorxiv.org/content/10.110…

Have any thoughts on what you would like to see highlighted in the next Galaxy Newsletter? Please let us know! We are interested in highlighting technical advances, scientific applications, and events. Thank you for taking the time to contribute! ➡️ forms.gle/XaWRJZPcem1wy1…

This is one of the most exciting project I've worked recently. Incredibly happy we are finally make it available on GitHub as open-source software. x.com/SeqeraLabs/sta…

Come and join our vibrant #core #bioinformatics team! Cool microbiomes and ourselves will welcome you 🙃

Absolutely delighted my 1st 1st author paper for complete & accurate phage genome assembly is officially out! This was a steep learning curve for a wet lab scientist & I'm extremely grateful to my supervisory team & all co-authors & collaborators! #PhD microbiologyresearch.org/content/journa…