João André Carriço

Microbial Bioinformatics by trade. Gamer 4 Life. Loves to solve a puzzle. The opinions expressed here are my own.

[Nabil-Fareed Alikhan @[email protected] @happy_khan]

# How to download SRA reads without wanting to die

python3 -m venv .venv
source .venv/bin/activate
pip install ffq
ffq --ftp ERRXXX | jq -r '.[] | .url' | xargs curl -O

[Migla Miskinyte @MMiskinyte]

Not so long left until the deadline! Apply by 15th of March to join us for SymbNET International Conference on Host-Microbe Symbiosis in the South of Portugal! See you there https://t.co/I4svPJgh6W 10th to 15th of June? @SymbNET #Olhao #Portugal @cellhostmicrobe @host_microbe

[João André Carriço @jacarrico]

@rrwick Great post Ryan! I assume from the data you provided your assemblies had a final coverage >250x. It would be great if you had random 70-100x coverages to compare as they would be closer to multiplexing several strains in a flow cell

[Ryan Wick @rrwick]

New blog post:
https://t.co/Kvkkb9ucNu

I revisit the question of ONT-only accuracy for bacterial genomes, and things have improved a lot since I last looked at this about six months ago!

[João André Carriço @jacarrico]

@branmorrighan Python….

[Heng Li @lh3lh3]

Wonder why the BUSCO completeness of T2T-CHM13 is only 95.7%? Tricky protein-to-genome alignment. Try miniBUSCO. It is 1) much faster, 2) more accurate for well annotated lineages, 3) robust to frameshift errors, and 4) more lightweight. Fine work by @csuhuangneng

[Sylvain Brisse @sylvainbrisse]

Position annoucement: Post-doc in my lab on the Genomic taxonomy of microbial strains. Please apply if you are fond of genomic surveillance of pathogens, international harmonization, dissemination of research, bioinformatics and public health https://t.co/ua76hOV2pC

[João André Carriço @jacarrico]

@johnrossen Respect!!! One of this years I will do the same…

[João André Carriço @jacarrico]

It very nice to be back to #ABPHM23 and meet old friends and make new ones! 12 y has passed since my first ABPHM ! It is also nice to see that everyone is still something nore than a 2D head, a icon or a disembodied voice in my computer!

[João André Carriço @jacarrico]

@sylvainbrisse @guwe33 @ESGEM_ESCMID Thank you @guwe33 ! A job well done and a great team throughout this times!

[Anusha Karunasagar MD PhD DipRCPath MBA CIC @AnushaRohit]

#ECCMID2023 AI in microbiology. The new future. Shouldn't we learn to adapt?

[guido werner @guwe33]

Plasmid replacement, not strain replacement is the case in Swiss poultry production concerning CTX-M1 to SHV-12 switch - great Talk by Dr Alessandra Carattoli at #ECCMID2023

[João André Carriço @jacarrico]

Do you remember when you joined Twitter? I do! #MyTwitterAnniversary (I actually didn’t and it was twitter that reminded me…)

[João André Carriço @jacarrico]

@torstenseemann I bet it is already tens of millions! A super tool for the community!

[Torsten Seemann @torstenseemann]

Prokka passed 10,000 citations on Google Scholar this week. It's mind-blowing to think it has annotated millions of bacterial genomes over the last 8 years. Thanks to everyone for your support and feedback. 💚🦠🧬💻

[Norelle Sherry @norelle_sherry]

Very excited to announce that our recent paper has been published in Nature Comms! - a 🧵https://t.co/f6CzpcNYgS
An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance
@BenjaminHowden @torstenseemann @KristyHoran14 @TheDohertyInst

[Inês Mendes @ines_cim]

I'm thrilled to announce that our latest work, "LMAS: evaluating metagenomic short de novo assembly methods through defined communities" has just been published in @GigaScience! 🥳🦠 Featuring @jacarrico @MoranGilad P. Vila-Cerqueira Y. Motro M. Ramirez
https://t.co/TkwFBtk20Q

[Duncan MacCannell @dmaccannell]

This is kind of amazing. Who wants to lay down a beat?

[João André Carriço @jacarrico]

@johnlees6 @sheppard_lab Epic! Made my day :-D

[João André Carriço @jacarrico]

@dmaccannell @sylvainbrisse Duncan, That is a typical IMMEM ;-)