https://github.com/thackl/utir-genome-pipeline

Assembly and annotation pipeline for UTIr project isolates
https://github.com/thackl/utir-genome-pipeline

Last synced: 8 months ago
JSON representation

Assembly and annotation pipeline for UTIr project isolates

• Host: GitHub
• URL: https://github.com/thackl/utir-genome-pipeline
• Owner: thackl
• Created: 2025-03-29T10:35:58.000Z (about 1 year ago)
• Default Branch: main
• Last Pushed: 2025-03-29T11:14:04.000Z (about 1 year ago)
• Last Synced: 2025-03-29T12:22:55.496Z (about 1 year ago)
• Language: Python
• Size: 109 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

          
Assembly, QC and Annotation pipeline for bacterial isolates collected as part of

the UTIr project.

# The pipeline comprises the following steps

- prescreen of sequencing libraries for contamination with `sylph` 

- assembly of long-reads with `flye`

- polishing with `medaka`

- completeness and contamination assessment with `checkm2`

- decontamination in flagged assemblies using a low coverage filter

- synchronization start and orientation of circular chromosomes

- taxonomic classification with `gtdbtk`

- gene prediction and annotation with `bakta`

- plasmid and (pro)virus annotation with `genomad`

![rulegraph](rulegraph.png)

# Input

The pipeline expects as input a folder `analysis/reads/` with compressed minion

fq.gz files.

# Dependencies and Databases

The pipeline is set up to use isolated rule-specific conda

environments. Dependencies, thus will be automatically installed once the

respective environment is is loaded/created for the first time. Databases are

automatically downloaded via post-deploy scripts when the respective

environments are used.