Projects per year
Description
This repository contains a Snakemake bacterial assembly QC pipeline to perform quality control. It will use Quast (metrics), CheckM2 (completedness and contamination), Busco (completedness), skANI (taxonomic assignment against GTDB with ANI). It will also produce a Busco plot summary, a beeswarm plot of N50 and number of contigs, and an excel file with Quast, CheckM2 and skANI summaries. The latest version of the scripts can be found at https://gitlab.ilvo.be/genomics/wgs/bacterial-assembly-qc-snakemake
Version
1.0.0
| Date made available | 30-Aug-2024 |
|---|---|
| Publisher | Zenodo |
| Date of data production | 30-Aug-2024 |
Keywords datasets
- assembly
- QC
- snakemake
Projects
- 2 Active
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EXORAL: Preparing for the introduction of exotic strains of the Ralstonia solanacearum species complex (i.e. of Ralstonia pseudosolanacearum and Ralstonia syzygii) – valorisation of culture collections and validation of diagnostics and methods for epidemiosurveillance
Venneman, J. (Project Manager), Van Vaerenbergh, J. (Researcher), Baeyen, S. (Project Assistant) & Slos, D. (Project Assistant)
1/05/24 → 30/04/26
Project: Research
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SOURCETRACK: Source identification of brown rot and ring rot infections in Belgium (1989-2021) by forensic investigation of bacterial genome sequences
Van Vaerenbergh, J. (Project Manager), Venneman, J. (Researcher), Baeyen, S. (Project Assistant) & De Paepe, B. (Project Assistant)
1/03/24 → 28/02/25
Project: Research