📢 Excited to announce that Phables now supports long-read assemblies!
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⭐️ Check out the new release: https://github.com/Vini2/phables/releases/tag/v1.3.0
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🧬 Feel free to test out Phables on your long-read assemblies of metagenomes, viromes or even isolates. 🦠🧫
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#Phages #Bacteriophages #Phables #Metagenomics #Bioinformatics #Software

Excited to share that we were awarded a 2024 National Computational Merit Allocation Scheme (NCMAS) supercomputing grant. 🖥️🥳🤩
@linsalrob @BeardyMcJohnFace @npbhavya @griggo_grig

https://my.nci.org.au/mancini/ncmas/2024/outcomes

#Bioinformatics #bacteriophages #HPC #software

Glad to see GraphBin contributing to discover new core genera in fermented red pepper sauce metagenomes.

#bioinformatics #metagenomics #binning #assemblygraphs

https://www.sciencedirect.com/science/article/pii/S221242922301074X

It was my great pleasure to talk about Phables at ABACBS 2023. Thanks for all the awesome feedback and chats! Also a big thank you to @abacbs for the opportunity and everyone from the FAME lab.
#abacbs2023 #bioinformatics

@naturepoker Thank you! 😃

I'm very excited to share that our bacteriophage recovery tool, Phables has been accepted for publication in the OUP Bioinformatics journal.

Publication: https://doi.org/10.1093/bioinformatics/btad586
GitHub: https://github.com/Vini2/phables

A big thank you to everyone at FAME for supporting this work.
@BeardyMcJohnFace @npbhavya @griggo_grig @GB13Faithless @AbbeyHutton @Sassel1985 @linsalrob

#bioinformatics #metagenomics #bacteriophages #assembly #assemblygraph #graphtheory #flownetworks

@griggo_grig from presenting Phynteny at APG Awards Fest. 🧬🦠🔬🌟 You can predict the functions of unknown phage genes using an LSTM model trained with phage synteny.
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Check out Phynteny at https://github.com/susiegriggo/Phynteny
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#phages #bacteriophages #synteny #APGAwardsFest2023

Excited to announce that the first stable release of Phables is now up on bioconda and PyPI. 🤩🧬 If you study phages in metagenomes give it a try. 😄
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Bioconda: https://anaconda.org/bioconda/phables
PyPI: https://pypi.org/project/phables/
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#Bioinformatics #metagenomics #phage #phage #bacteriophage

RT @EVirusBioinfC
We are happy to announce the final speaker in our list of keynote speakers! Rob Edwards @linsalrob will join us in Valencia at #ViBioM2023 to speak about the promise and pitfalls of #prophages. Registration is still open: https://evbc.uni-jena.de/events/vibiom2023/registration/

The preprint of Phables is up on biorxiv! Phables can resolve high-quality bacteriophage genomes from fragmented metagenome assemblies using assembly graphs.

Preprint: https://www.biorxiv.org/content/10.1101/2023.04.04.535632v1
GitHub: https://github.com/Vini2/phables

@BeardyMcJohnFace @npbhavya @griggo_grig @GB13Faithless @AbbeyHutton @linsalrob

#bacteriophages #phages #metagenomics #bioinformatics #software

Phables: from fragmented assemblies to high-quality bacteriophage genomes https://www.biorxiv.org/content/10.1101/2023.04.04.535632v1?med=mas

Excited to see that GraphBin and its successors have inspired better tools and the use of assembly graphs to improve metagenome-assembled genomes. Check out UGMAGrefiner.

https://www.sciencedirect.com/science/article/pii/S2001037023001265

#Bioinformatics #metagenomics #mags #Software

Our stingray microbiomes paper is now available on Frontiers in Microbiology. Congratulation Emma! Glad to see GraphBin contributing to scientific knowledge. 😃🦠🧬💻

https://www.frontiersin.org/articles/10.3389/fmicb.2023.1031711/full

#stingray #microbiome #metagenomics #Bioinformatics

A new version of GraphBin is now available on bioconda, including support for original contigs from Flye assemblies.

https://anaconda.org/bioconda/graphbin

#Bioinformatics #graphbin #software #metagenomics #binning

Today I stumbled upon Grayskull (https://github.com/conda-incubator/grayskull) an automatic conda recipe generator. 💀

I used `conda skeleton` to generate a recipe for one of my PyPI projects and it didn't work. My project uses a pyproject.toml file which has now replaced the traditional setup.py. However, `conda skeleton pypi` still requires a setup.py and fails if your project does not have one. Grayskull can work with pyproject.toml. It saved my day. Hope it will be useful to you too. 😀

#software #python #conda

Starting off 2023 by learning Snakemake and made one of my tools into a full pipeline using Snaketool, the Cookiecutter profile for making Snakemake-based bioinformatics tools. 🐍😀

If you want to resolve phage genomes from viral metagenomic samples, go check out my new tool Phables on bioconda! 😃

Phables: https://anaconda.org/bioconda/phables
Snaketool: https://github.com/beardymcjohnface/Snaketool

#Bioinformatics #Software #Bacteriophages #Phages

Our first publication of 2023 is now out in Frontiers in Microbiology. We study the composition and metabolism of microbial communities in Daqu, the Chinese liquor fermentation starter.
#Bioinformatics #metaproteomics #research #analysis
https://www.frontiersin.org/articles/10.3389/fmicb.2022.1098268/full

New paper is out! Writing research software is hard, so why make it harder than it needs to be? https://doi.org/10.1371/journal.pcbi.1010705 Thank you to all my amazing collaborators @saltyscientist@twitter.com @bioinforad @vijinim @npbhavya @ctb @watsonhaigh@twitter.com @linsalrob #bioinformatics

Getting ready for a phage-tastic Christmas with Rudolph the red-nosed phage-deer 🎄🤩
@linsalrob @BeardyMcJohnFace @npbhavya @griggo_grig @Sassel1985 @AbbeyHutton
Template credits go to Dr Siân V. Owen https://scholar.harvard.edu/sianowen/paper-bacteriophage-template
#phages #bacteria #microbes #Christmas

My latest article on Medium walks you through how to publish Python packages of bioinformatics software on Bioconda. 🐍👩🏻‍💻
#Bioinformatics #bioconda #Python #Software
https://towardsdatascience.com/all-you-need-to-know-about-publishing-software-on-bioconda-680d48e52868?sk=bcd00f3bedb4638239e6f35779c6638b