Nabil-Fareed Alikhan

@[email protected]
1.6K Followers
941 Following
1.3K Posts
Admin for @mstdn.science. #bioinformatician. Interested in #microbiology and #genomics.
Websitehttp://happykhan.com
Twitterhttps://twitter.com/happy_khan
GitHubhttps://github.com/happykhan
Nabil-Fareed Alikhan4d ago
Snakemake Release Robot4d ago

Beep, Beep - I am your friendly #Snakemake release announcement bot.

There is a new release of the ๐’๐ง๐š๐ค๐ž๐ฆ๐š๐ค๐ž ๐„๐ฑ๐ž๐œ๐ฎ๐ญ๐จ๐ซ ๐๐ฅ๐ฎ๐ ๐ข๐ง ๐Ÿ๐จ๐ซ ๐’๐‹๐”๐‘๐Œ systems. Its version now is 2.6.0!

Give us some time, and you will automatically find the plugin on #Bioconda and #Pypi.

This plugin is relevant for #HPC users using the #SLURM batch system.
The maintainers are here on Mastodon -
@rupdecat and @johanneskoester.

If you discover any issues, please report them on https://github.com/snakemake/snakemake-executor-plugin-slurm/issues.

See https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v2.6.0 for details. Here is the header of the changelog:
๐‘…๐‘’๐‘™๐‘’๐‘Ž๐‘ ๐‘’ ๐‘๐‘œ๐‘ก๐‘’๐‘  (๐‘๐‘œ๐‘ ๐‘ ๐‘–๐‘๐‘™๐‘ฆ ๐‘Ž๐‘๐‘๐‘Ÿ๐‘–๐‘”๐‘’๐‘‘):
๐…๐ž๐š๐ญ๐ฎ๐ซ๐ž๐ฌ

* job arrays: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/174
* Set tmpspace with help of gres="tmpspace:10G" syntax: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/444

๐๐ฎ๐  ๐…๐ข๐ฑ๐ž๐ฌ

* logo: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/439

๐ƒ๐จ๐œ๐ฎ๐ฆ๐ž๐ง๐ญ๐š๐ญ๐ข๐จ๐ง

* add admin documentation: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/436

Nabil-Fareed Alikhan4d ago

Host read removal sounds simple. It's not. ๐ŸงซEp. 151 of microbinfie: we talk with Bede Constantinides about Deacon โ€” why alignment-based approaches fall short, the sensitivity/specificity tradeoff, and what it takes to remove host reads at scale. Part 1 of 2.

https://soundcloud.com/microbinfie/151-deacon-part-1

151 - Deacon part 1

In this Software Deep Dive episode, we talk with Dr. Bede Constantinides (University of Birmingham) about Deacon, a tool for removing host DNA reads from metagenomic datasets. We discuss why host read

SoundCloud
Show threadNabil-Fareed Alikhan5d ago

the web application is available at :

https://brigx.genomicx.org/

I would be interested to hear feedback regarding bugs or any unexpected behaviour, any suggestions for the user interface, or any features you feel would be useful .

BRIGX - Browser-Based Ring Image Generator

Circular comparative genome visualization tool running entirely in your browser

Nabil-Fareed Alikhan5d ago

Been working on a browser version of BRIG. No install. Interactive. Looking for beta testers; message me if you're interested.

BRIG Is a visualisation tool that draws circular genome comparison plots. The user provides a reference genome and a set of query genomes which are aligned using BLAST. Genomes are bacteria sized (< 20Mbp). Colour gradient shows alignment identity. Users can also provide tables of coordinates for their own annotations on the plot.

Nabil-Fareed AlikhanMar 12
Bye bye research fish
Nabil-Fareed AlikhanMar 7

We just uploaded the 150th episode of the #microbinfie podcast, scheduled for Thursday, where we blow your mind with vibe coding. I can't believe we have actually made it this far.

๐Ÿป To the next 150 episodes ๐Ÿฅ‚

https://soundcloud.com/microbinfie

Micro Binfie Podcast

Microbial Bioinformatics is a rapidly changing field marrying computer science and microbiology. Join us as we share some tips and tricks weโ€™ve learnt over the years. If youโ€™re student just getting to

SoundCloud
Nabil-Fareed AlikhanMar 5
Centre for Genomic Pathogen SurveillanceMar 5
Reporting from the AMR Surveillance Convening at Africa CDC, Addis Ababa. Opening message was direct: the surveillance gap isn't about knowledge anymore, it's delivery and financing. Africa carries ~21% of the global AMR burden. Recap of Day 1 from www.amrsurveillance.org #AMRSurveillanceAddis

AMR Convening on Building Sust...
AMR Convening on Building Sustainable AMR Genomic Surveillance

A focused convening to identify practical pathways for strengthening routine national AMR surveillance systems, including the integration of genomic data.

Nabil-Fareed AlikhanMar 5
Centre for Genomic Pathogen SurveillanceMar 3
Nearly 90% of AMR pathogen genomes come from high-income countries.109 participants from 52 countries meeting in Addis Ababa to close this gap. www.amrsurveillance.org #AMR #HealthEquity #Genomics #AMRSurveillanceAddis

AMR Convening on Building Sust...
AMR Convening on Building Sustainable AMR Genomic Surveillance

A focused convening to identify practical pathways for strengthening routine national AMR surveillance systems, including the integration of genomic data.

Nabil-Fareed AlikhanMar 5
Centre for Genomic Pathogen SurveillanceMar 5
Sentinel site session was the most grounding. Surveillance fails when it's extractive โ€” data goes up, nothing comes back. Labs engage when it improves their own practice. www.amrsurveillance.org #AMRSurveillanceAddis
Nabil-Fareed AlikhanMar 5
Centre for Genomic Pathogen SurveillanceMar 5
Four national stories. Philippines: 38 years of AMR surveillance, now adding WGS. Uganda: 16 to 43 sites. Pakistan: building a genomic strategy. Brazil: mapping labs nationally. Start small, invest in quality, build government ownership. #AMRSurveillanceAddis Day 1 of www.amrsurveillance.org