Greg Fedewa
@science.ninja
Bioinformatic Scientist interested in microbes. Former: Ismagilov Group (Caltech), Nuanced Health Inc; The Centre for Pathogen Evolution (U Cambridge, UK), DeRisi Lab (UCSF).
Pinned
Greg Fedewa
@science.ninja
· Jun 6
My time as a Bioinformatics Staff scientist at CalTech is coming to a close and I am looking for the next thing. If you need someone with plenty of experience in sequencing analysis, and pipeline building (Nextflow), please connect. I'm hoping to go back to industry but open to anything interesting.
So glad that a feature I've wanted, and then worked on, is finally out!
Run all the bin QC tools now!
Run all the bin QC tools now!
Pipeline release! nf-core/mag v5.2.0 - mag 5.2.0 - Puce Pangolin!
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.2.0
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.2.0
Release mag 5.2.0 - Puce Pangolin · nf-core/mag
Added
#842 - Add support for running multiple binQC tools in one run using dedicated --run_busco, --run_checkm, and --run_checkm2 parameters (by @harper357, with contributions from @dialvarezs, @p...
github.com
November 7, 2025 at 8:29 PM
So glad that a feature I've wanted, and then worked on, is finally out!
Run all the bin QC tools now!
Run all the bin QC tools now!
Reposted by Greg Fedewa
🚨PhD opportunity at the intersection of computation & biology! 🖥️🧬🧪
Ready to tackle complex biological problems with cutting-edge tools? The BMI PhD program @UCSF trains future leaders in comp bio, bioinformatics, & data science.
📢 Info session: 11/6 @ 1 PM PT
bmi.ucsf.edu/admissions
Learn more👇
Ready to tackle complex biological problems with cutting-edge tools? The BMI PhD program @UCSF trains future leaders in comp bio, bioinformatics, & data science.
📢 Info session: 11/6 @ 1 PM PT
bmi.ucsf.edu/admissions
Learn more👇
October 24, 2025 at 6:26 PM
🚨PhD opportunity at the intersection of computation & biology! 🖥️🧬🧪
Ready to tackle complex biological problems with cutting-edge tools? The BMI PhD program @UCSF trains future leaders in comp bio, bioinformatics, & data science.
📢 Info session: 11/6 @ 1 PM PT
bmi.ucsf.edu/admissions
Learn more👇
Ready to tackle complex biological problems with cutting-edge tools? The BMI PhD program @UCSF trains future leaders in comp bio, bioinformatics, & data science.
📢 Info session: 11/6 @ 1 PM PT
bmi.ucsf.edu/admissions
Learn more👇
How does everyone keep track of where they left off when reading #QuartoPub book websites? Is there an Quarto or browser extension ? I have a browser bookmark to the main page, but (ideally) I would want some button i click to go to my "bookmarked" page.
September 30, 2025 at 5:21 PM
How does everyone keep track of where they left off when reading #QuartoPub book websites? Is there an Quarto or browser extension ? I have a browser bookmark to the main page, but (ideally) I would want some button i click to go to my "bookmarked" page.
Does anyone know of non-profits, consortiums, labs, or groups that focus on genome sequencing rare/endangered plants? I can't seem to find anything, but it seems like this should exist. I am only finding groups that sequenced a single rare species or two. 🌱🧪 #plantsky #academicsky
August 26, 2025 at 11:24 PM
Does anyone know of non-profits, consortiums, labs, or groups that focus on genome sequencing rare/endangered plants? I can't seem to find anything, but it seems like this should exist. I am only finding groups that sequenced a single rare species or two. 🌱🧪 #plantsky #academicsky
It's wild to me how horrible it still is to apply for a job. Do you really need to know the exact date I started my last job? Your site needs me to manually enter my full resume even after I just uploaded it? Your screener looked for Pandas instead of pandas?
June 18, 2025 at 8:21 PM
It's wild to me how horrible it still is to apply for a job. Do you really need to know the exact date I started my last job? Your site needs me to manually enter my full resume even after I just uploaded it? Your screener looked for Pandas instead of pandas?
Reposted by Greg Fedewa
My time as a Bioinformatics Staff scientist at CalTech is coming to a close and I am looking for the next thing. If you need someone with plenty of experience in sequencing analysis, and pipeline building (Nextflow), please connect. I'm hoping to go back to industry but open to anything interesting.
June 6, 2025 at 6:40 PM
My time as a Bioinformatics Staff scientist at CalTech is coming to a close and I am looking for the next thing. If you need someone with plenty of experience in sequencing analysis, and pipeline building (Nextflow), please connect. I'm hoping to go back to industry but open to anything interesting.
My time as a Bioinformatics Staff scientist at CalTech is coming to a close and I am looking for the next thing. If you need someone with plenty of experience in sequencing analysis, and pipeline building (Nextflow), please connect. I'm hoping to go back to industry but open to anything interesting.
June 6, 2025 at 6:40 PM
My time as a Bioinformatics Staff scientist at CalTech is coming to a close and I am looking for the next thing. If you need someone with plenty of experience in sequencing analysis, and pipeline building (Nextflow), please connect. I'm hoping to go back to industry but open to anything interesting.
I'm excited to see my contributions made it into this version! It was a lot easier to add new modules than I expected. If anyone is wishing a tool was supported, you should just try adding it.
🆕 10 new modules supporting new tools in this release:
- MosaiCatcher
- ataqv
- telseq
- Cell
- GTDB
- Checkm
- Checkm2
- Haplocheck
- mgikit
- Percolator
- MosaiCatcher
- ataqv
- telseq
- Cell
- GTDB
- Checkm
- Checkm2
- Haplocheck
- mgikit
- Percolator
December 23, 2024 at 2:57 AM
I'm excited to see my contributions made it into this version! It was a lot easier to add new modules than I expected. If anyone is wishing a tool was supported, you should just try adding it.
Does anyone have some good resources on research-backed best practices for data plotting? I want to put together a document or short talk to help standardize figures generated in the lab and will have to counter a lot of "this is how [big lab] did it in their paper". #stats #datavis
November 20, 2024 at 6:51 PM
I wish the ability to mute an account was still an option on posts. It made muting so much easier and I don't understand why it was removed.
October 23, 2024 at 1:32 AM
I wish the ability to mute an account was still an option on posts. It made muting so much easier and I don't understand why it was removed.