Linda van der Graaf
@lindavdgraaf.bsky.social
Assistant professor at Utrecht University the Netherlands, Biomolecular Health Sciences.
AMR | Campylobacter | Pathogen genomics
AMR | Campylobacter | Pathogen genomics
Reposted by Linda van der Graaf
We happily present: “Bakta Web – rapid and standardized genome annotation on scalable infrastructures” @OxUniPress NAR’s Web Server issue
doi.org/10.1093/nar/...
Easy to use, no registration, fast, scalable, various visualizations, in sync with Bakta CLI:
bakta.computational.bio
(1/5)
doi.org/10.1093/nar/...
Easy to use, no registration, fast, scalable, various visualizations, in sync with Bakta CLI:
bakta.computational.bio
(1/5)
Bakta Web – rapid and standardized genome annotation on scalable infrastructures
Abstract. The Bakta command line application is widely used and one of the most established tools for bacterial genome annotation. It balances comprehensiv
doi.org
April 28, 2025 at 8:47 AM
We happily present: “Bakta Web – rapid and standardized genome annotation on scalable infrastructures” @OxUniPress NAR’s Web Server issue
doi.org/10.1093/nar/...
Easy to use, no registration, fast, scalable, various visualizations, in sync with Bakta CLI:
bakta.computational.bio
(1/5)
doi.org/10.1093/nar/...
Easy to use, no registration, fast, scalable, various visualizations, in sync with Bakta CLI:
bakta.computational.bio
(1/5)
Reposted by Linda van der Graaf
🦠🧬🖥️ New Bakta DB v6.0 released!
After a year, it was time for a Bakta database update - and it's a huge one:
- IPS: 330.9M
- PSC: 135.3M
- PSCC: 37M
doi.org/10.5281/zeno...
👇 1/6
After a year, it was time for a Bakta database update - and it's a huge one:
- IPS: 330.9M
- PSC: 135.3M
- PSCC: 37M
doi.org/10.5281/zeno...
👇 1/6
Bakta database
This data repository contains the mandatory DB for Bakta. It is available in two versions: the default (db.tar.gz or) and a lightweight alternative (db-light.tar.gz). Bakta is a tool for the rapid & s...
doi.org
March 6, 2025 at 8:59 AM
🦠🧬🖥️ New Bakta DB v6.0 released!
After a year, it was time for a Bakta database update - and it's a huge one:
- IPS: 330.9M
- PSC: 135.3M
- PSCC: 37M
doi.org/10.5281/zeno...
👇 1/6
After a year, it was time for a Bakta database update - and it's a huge one:
- IPS: 330.9M
- PSC: 135.3M
- PSCC: 37M
doi.org/10.5281/zeno...
👇 1/6
Reposted by Linda van der Graaf
New preprint is out!
We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling.
Read it here: www.biorxiv.org/content/10.1...
Data & code: github.com/rrwick/Are-r...
(1/8)
We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling.
Read it here: www.biorxiv.org/content/10.1...
Data & code: github.com/rrwick/Are-r...
(1/8)
Are reads required? High-precision variant calling from bacterial genome assemblies
Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared...
www.biorxiv.org
March 3, 2025 at 3:24 AM
New preprint is out!
We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling.
Read it here: www.biorxiv.org/content/10.1...
Data & code: github.com/rrwick/Are-r...
(1/8)
We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling.
Read it here: www.biorxiv.org/content/10.1...
Data & code: github.com/rrwick/Are-r...
(1/8)
Reposted by Linda van der Graaf
Center for Molecular Medicine at UMC Utrecht is looking for a Principal Investigator in the field of fundamental Cancer Biology! The vacancy states tenure track level, but also candidates with a more advanced career are very welcome to apply.
www.werkenbijumcutrecht.nl/vacatures/we...
www.werkenbijumcutrecht.nl/vacatures/we...
Center for Molecular Medicine
cmmutrecht.eu
March 3, 2025 at 8:29 PM
Center for Molecular Medicine at UMC Utrecht is looking for a Principal Investigator in the field of fundamental Cancer Biology! The vacancy states tenure track level, but also candidates with a more advanced career are very welcome to apply.
www.werkenbijumcutrecht.nl/vacatures/we...
www.werkenbijumcutrecht.nl/vacatures/we...
Reposted by Linda van der Graaf
🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again!
forms.gle/YJP6WQjsk8KK...
forms.gle/YJP6WQjsk8KK...
Snippy: Microbial Variant Calling Community Survey
Help us drive the next wave of innovation in Single-Nucleotide Polymorphism (SNP) discovery and genome analysis by sharing your valuable experiences and insights. This in-depth survey aims at understa...
forms.gle
March 4, 2025 at 9:04 AM
🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again!
forms.gle/YJP6WQjsk8KK...
forms.gle/YJP6WQjsk8KK...