Robert Petit
@rpetit3.bsky.social
Public health bacterial genomics, bioinformatic workflow development, and training. Bactopia (https://bactopia.github.io). @ Wyoming Public Health Laboratory
Seems I'm not good at Bactopia v4 progress updates!
Since my last update:
- Nextflow v25+ compatible
- Converted to nf-test
- nf-bactopia plugin released
If you are interesting in testing (very much appreciated!), I now have a dev build available here: github.com/bactopia/bac...
Since my last update:
- Nextflow v25+ compatible
- Converted to nf-test
- nf-bactopia plugin released
If you are interesting in testing (very much appreciated!), I now have a dev build available here: github.com/bactopia/bac...
Bactopia v4 - Overview & Help Wanted · Issue #628 · bactopia/bactopia
Bactopia v4 Yo! Well, it is about that time! I am planning to release version 4 of Bactopia in the near future. With this version, Bactopia will introduce new and exciting things, but at the same t...
github.com
October 6, 2025 at 8:31 PM
Seems I'm not good at Bactopia v4 progress updates!
Since my last update:
- Nextflow v25+ compatible
- Converted to nf-test
- nf-bactopia plugin released
If you are interesting in testing (very much appreciated!), I now have a dev build available here: github.com/bactopia/bac...
Since my last update:
- Nextflow v25+ compatible
- Converted to nf-test
- nf-bactopia plugin released
If you are interesting in testing (very much appreciated!), I now have a dev build available here: github.com/bactopia/bac...
Reposted by Robert Petit
Mirrors! 🪞
I created a site to download and host small datasets in mirrors in the github pages space. Therefore, any region that github has better connectivity to would be able to download more quickly.
I started with NCBI taxonomy. What else? lskatz.github.io/mirror/
I created a site to download and host small datasets in mirrors in the github pages space. Therefore, any region that github has better connectivity to would be able to download more quickly.
I started with NCBI taxonomy. What else? lskatz.github.io/mirror/
Mirrors
This is an attempt to make a mirror for some commonly used bioinformatics datasets.
lskatz.github.io
September 7, 2025 at 2:33 AM
Mirrors! 🪞
I created a site to download and host small datasets in mirrors in the github pages space. Therefore, any region that github has better connectivity to would be able to download more quickly.
I started with NCBI taxonomy. What else? lskatz.github.io/mirror/
I created a site to download and host small datasets in mirrors in the github pages space. Therefore, any region that github has better connectivity to would be able to download more quickly.
I started with NCBI taxonomy. What else? lskatz.github.io/mirror/
Another Bactopia update!
I think the plugin is completed now! I've also started the transition from pytest to nf-test (from @lukfor.bsky.social and @sebschoenherr.bsky.social). So far nf-test has been great to work with! Haha probably should have made the transition a long time ago!
I think the plugin is completed now! I've also started the transition from pytest to nf-test (from @lukfor.bsky.social and @sebschoenherr.bsky.social). So far nf-test has been great to work with! Haha probably should have made the transition a long time ago!
August 26, 2025 at 7:44 PM
Another Bactopia update!
I think the plugin is completed now! I've also started the transition from pytest to nf-test (from @lukfor.bsky.social and @sebschoenherr.bsky.social). So far nf-test has been great to work with! Haha probably should have made the transition a long time ago!
I think the plugin is completed now! I've also started the transition from pytest to nf-test (from @lukfor.bsky.social and @sebschoenherr.bsky.social). So far nf-test has been great to work with! Haha probably should have made the transition a long time ago!
Bactopia update!
Bactopia is now compatible with @nextflow.io v25 syntax and the plugin (github.com/bactopia/nf-...) is converted to the latest structure. I'm hoping to have a development build soon.
If you're interested in testing please let me know here or at github.com/bactopia/bac...
Bactopia is now compatible with @nextflow.io v25 syntax and the plugin (github.com/bactopia/nf-...) is converted to the latest structure. I'm hoping to have a development build soon.
If you're interested in testing please let me know here or at github.com/bactopia/bac...
August 13, 2025 at 11:27 PM
Bactopia update!
Bactopia is now compatible with @nextflow.io v25 syntax and the plugin (github.com/bactopia/nf-...) is converted to the latest structure. I'm hoping to have a development build soon.
If you're interested in testing please let me know here or at github.com/bactopia/bac...
Bactopia is now compatible with @nextflow.io v25 syntax and the plugin (github.com/bactopia/nf-...) is converted to the latest structure. I'm hoping to have a development build soon.
If you're interested in testing please let me know here or at github.com/bactopia/bac...
Reposted by Robert Petit
skani v0.3.0 is released. github.com/bluenote-157...
- 30-40% potential reduction in memory with approximately the same runtime.
- Breaking changes to indexing and searching databases
Calculate ANI for contigs, genomes -- even search > 140k genomes. Pre-indexed GTDB-R226 available for download.
- 30-40% potential reduction in memory with approximately the same runtime.
- Breaking changes to indexing and searching databases
Calculate ANI for contigs, genomes -- even search > 140k genomes. Pre-indexed GTDB-R226 available for download.
GitHub - bluenote-1577/skani: Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs. - bluenote-1577/skani
github.com
August 13, 2025 at 2:19 PM
skani v0.3.0 is released. github.com/bluenote-157...
- 30-40% potential reduction in memory with approximately the same runtime.
- Breaking changes to indexing and searching databases
Calculate ANI for contigs, genomes -- even search > 140k genomes. Pre-indexed GTDB-R226 available for download.
- 30-40% potential reduction in memory with approximately the same runtime.
- Breaking changes to indexing and searching databases
Calculate ANI for contigs, genomes -- even search > 140k genomes. Pre-indexed GTDB-R226 available for download.
Minor Bactopia v4 update, I have a first pass at the Nextflow v25 syntax conversion.
I converted a Bactopia Tool to v25, then used @anthropic.com Claude to some help convert the remaining Bactopia Tools.
Lots of cleaning still, but progress!
See github.com/bactopia/bac... for details on v4!
I converted a Bactopia Tool to v25, then used @anthropic.com Claude to some help convert the remaining Bactopia Tools.
Lots of cleaning still, but progress!
See github.com/bactopia/bac... for details on v4!
August 12, 2025 at 4:59 AM
Minor Bactopia v4 update, I have a first pass at the Nextflow v25 syntax conversion.
I converted a Bactopia Tool to v25, then used @anthropic.com Claude to some help convert the remaining Bactopia Tools.
Lots of cleaning still, but progress!
See github.com/bactopia/bac... for details on v4!
I converted a Bactopia Tool to v25, then used @anthropic.com Claude to some help convert the remaining Bactopia Tools.
Lots of cleaning still, but progress!
See github.com/bactopia/bac... for details on v4!
Howdy! I'm currently writing up version 4 of Bactopia!
Similar to previous major versions, I've started an issue on Github to track v4 progress. If you are a user of Bactopia and would like to help with feedback or with code, check out the following link:
github.com/bactopia/bac...
Similar to previous major versions, I've started an issue on Github to track v4 progress. If you are a user of Bactopia and would like to help with feedback or with code, check out the following link:
github.com/bactopia/bac...
Bactopia v4 - Overview & Help Wanted · Issue #628 · bactopia/bactopia
Bactopia v4 Yo! Well, it is about that time! I am planning to release version 4 of Bactopia in the near future. With this version, Bactopia will introduce new and exciting things, but at the same t...
github.com
August 6, 2025 at 8:20 PM
Howdy! I'm currently writing up version 4 of Bactopia!
Similar to previous major versions, I've started an issue on Github to track v4 progress. If you are a user of Bactopia and would like to help with feedback or with code, check out the following link:
github.com/bactopia/bac...
Similar to previous major versions, I've started an issue on Github to track v4 progress. If you are a user of Bactopia and would like to help with feedback or with code, check out the following link:
github.com/bactopia/bac...
Reposted by Robert Petit
Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight)
interpretamr.github.io/AMRrules
interpretamr.github.io/AMRrules
May 22, 2025 at 9:35 AM
Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight)
interpretamr.github.io/AMRrules
interpretamr.github.io/AMRrules
Reposted by Robert Petit
Dehosting compressed FASTQ at 150Mbp/s on a MacBook
github.com/bede/deacon
github.com/bede/deacon
May 9, 2025 at 2:23 PM
Dehosting compressed FASTQ at 150Mbp/s on a MacBook
github.com/bede/deacon
github.com/bede/deacon
At #APHL annual conference? Check out poster 212 to learn more about Bactopia and all the fun things it can do!
Side note, this is the first time all of Bactopia is depicted in a single metro map! 🎉
@bactopia.com @nextflow.io @aphl.org
Full PDF: datasets.bactopia.com/media/2025-b...
Side note, this is the first time all of Bactopia is depicted in a single metro map! 🎉
@bactopia.com @nextflow.io @aphl.org
Full PDF: datasets.bactopia.com/media/2025-b...
May 6, 2025 at 3:52 PM
At #APHL annual conference? Check out poster 212 to learn more about Bactopia and all the fun things it can do!
Side note, this is the first time all of Bactopia is depicted in a single metro map! 🎉
@bactopia.com @nextflow.io @aphl.org
Full PDF: datasets.bactopia.com/media/2025-b...
Side note, this is the first time all of Bactopia is depicted in a single metro map! 🎉
@bactopia.com @nextflow.io @aphl.org
Full PDF: datasets.bactopia.com/media/2025-b...
I've made a new framework for developing sequence based typing (SBT) tools.
🐪camlhmp ("camel hump") allows for an SBT schema to be defined in YAML, disentangling the SBT logic from the code, making much easier to maintain.
See poster or learn more at: rpetit3.github.io/camlhmp/late...
🐪camlhmp ("camel hump") allows for an SBT schema to be defined in YAML, disentangling the SBT logic from the code, making much easier to maintain.
See poster or learn more at: rpetit3.github.io/camlhmp/late...
October 21, 2024 at 3:19 AM
I've made a new framework for developing sequence based typing (SBT) tools.
🐪camlhmp ("camel hump") allows for an SBT schema to be defined in YAML, disentangling the SBT logic from the code, making much easier to maintain.
See poster or learn more at: rpetit3.github.io/camlhmp/late...
🐪camlhmp ("camel hump") allows for an SBT schema to be defined in YAML, disentangling the SBT logic from the code, making much easier to maintain.
See poster or learn more at: rpetit3.github.io/camlhmp/late...
Thankful for the opportunity to talk at #ASMNGS about the work we're doing at the WPHL 🦬 to further improve Bactopia! (haha also🏔️!)
Per the usual, reach out if you have any questions!
Slides are available at: bactopia.github.io/latest/impac...
Per the usual, reach out if you have any questions!
Slides are available at: bactopia.github.io/latest/impac...
October 21, 2024 at 3:18 AM
Thankful for the opportunity to talk at #ASMNGS about the work we're doing at the WPHL 🦬 to further improve Bactopia! (haha also🏔️!)
Per the usual, reach out if you have any questions!
Slides are available at: bactopia.github.io/latest/impac...
Per the usual, reach out if you have any questions!
Slides are available at: bactopia.github.io/latest/impac...
Reposted by Robert Petit
I thought the #ASMNGS #Hackathon was really productive. My team looked for unique markers for F. tularensis in WGS data and we were able to package everything into a github repository that's mostly functional. Thank you @meganphillips.bsky.social and my other teammates!
💻🧫🧬
💻🧫🧬
GitHub - erinyoung/tulatyper: Subtyping of Francisella tularensis subtypes
Subtyping of Francisella tularensis subtypes. Contribute to erinyoung/tulatyper development by creating an account on GitHub.
github.com
October 12, 2024 at 9:09 PM
I thought the #ASMNGS #Hackathon was really productive. My team looked for unique markers for F. tularensis in WGS data and we were able to package everything into a github repository that's mostly functional. Thank you @meganphillips.bsky.social and my other teammates!
💻🧫🧬
💻🧫🧬
👋 Bactopia users! After 5 years of maintaining Bactopia, I need your help!
What's next for Bactopia? 🔍 ⁉️
Help shape the next 5 years of Bactopia by filling out this quick survey: forms.gle/2nsFSYJtJ1me...
Please repost and share link with colleagues that also use Bactopia! 🎉
What's next for Bactopia? 🔍 ⁉️
Help shape the next 5 years of Bactopia by filling out this quick survey: forms.gle/2nsFSYJtJ1me...
Please repost and share link with colleagues that also use Bactopia! 🎉
Bactopia Usage Survey 2024
Yo! It's me Robert, the developer of Bactopia!
Did you know Bactopia has been maintained for over 5 years? Time flies! While I'm very grateful to have support to continue developing Bactopia, after 5...
forms.gle
March 27, 2024 at 2:17 PM
👋 Bactopia users! After 5 years of maintaining Bactopia, I need your help!
What's next for Bactopia? 🔍 ⁉️
Help shape the next 5 years of Bactopia by filling out this quick survey: forms.gle/2nsFSYJtJ1me...
Please repost and share link with colleagues that also use Bactopia! 🎉
What's next for Bactopia? 🔍 ⁉️
Help shape the next 5 years of Bactopia by filling out this quick survey: forms.gle/2nsFSYJtJ1me...
Please repost and share link with colleagues that also use Bactopia! 🎉
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/...
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/...
March 26, 2024 at 12:59 AM
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/...
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/...
🎉 Bactopia v3 is here! 🎉
Very excited for this release! Bactopia, the Nextflow pipeline for bacterial genomes, is now faster, packed with more tools, updated docs, and much much more!
Many thanks to all the people who helped test and provided feedback!
Learn more at: bactopia.github.io/v3.0.0/
Very excited for this release! Bactopia, the Nextflow pipeline for bacterial genomes, is now faster, packed with more tools, updated docs, and much much more!
Many thanks to all the people who helped test and provided feedback!
Learn more at: bactopia.github.io/v3.0.0/
Introduction - Bactopia
An extensive workflow to process Nanopore and Illumina sequencing for bacterial genomes.
bactopia.github.io
September 11, 2023 at 6:25 PM
🎉 Bactopia v3 is here! 🎉
Very excited for this release! Bactopia, the Nextflow pipeline for bacterial genomes, is now faster, packed with more tools, updated docs, and much much more!
Many thanks to all the people who helped test and provided feedback!
Learn more at: bactopia.github.io/v3.0.0/
Very excited for this release! Bactopia, the Nextflow pipeline for bacterial genomes, is now faster, packed with more tools, updated docs, and much much more!
Many thanks to all the people who helped test and provided feedback!
Learn more at: bactopia.github.io/v3.0.0/