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Published May 8, 2024 | Version v1.1.5
Software Open

BacFlux: A workflow for bacterial short reads assembly, QC, annotation, and more.

Authors/Creators

  • 1. AIT Austrian Institute of Technology
  • 2. IPK Leibniz Institute of Plant Genetics and Crop Plant Research

Description

BacFlux is a comprehensive and automated bioinformatics workflow designed specifically for the processing and analysis of bacterial genomic data sequenced with Illumina technology. It integrates several powerful tools, each performing a specific task, into a seamless workflow managed by a Snakemake script. The pipeline accepts paired-end reads as input and subjects them to a series of analyses including steps for quality control, assessment of genome completeness and contamination, taxonomic placement, annotation, inference of secondary metabolites, screening for antimicrobial resistance and virulence genes, and investigation of plasmid presence.

Files

iLivius/BacFlux-v1.1.5.zip

Files (145.8 kB)

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Additional details

Related works

Is supplement to
Software: https://github.com/iLivius/BacFlux/tree/v1.1.5 (URL)

Dates

Available
2024-05-08

Software

Repository URL
https://github.com/iLivius/BacFlux
Programming language
Python , Snakemake , Shell
Development Status
Active