| This repository contains a set of analysis tools for processing bacterial sequencing data.
The included tools are: 1) fastp & Bracken parser: Converts JSON reports from fastp and Bracken into structured CSV files. 2) QUAST & Shovill parser: Extracts QUAST metrics and converts contigs from Shovill into FASTA format. 3) MLST, AMRFinder, & STARamr parser: Processes MLST results and extracts antimicrobial resistance (AMR) gene data. These tools are designed for seamless integration into the Galaxy platform. They were developed as part of the SPAMR-VET/SA08 project: "Surveillance of Pathogens of Veterinary Importance and Their Antimicrobial Resistance Profiles" (O01 Action 4), conducted within the framework of the European Partnership on Animal Health and Welfare (EUP AH&W). |
hg clone https://toolshed.g2.bx.psu.edu/repos/maciek/spamr_vet_tools
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Extracts MLST, AMRfinder Plus, and STARamr results from JSON input. | 0.1.0+galaxy0 | 21.05 | |
| Quality control using FastP and Bracken | 0.1.0+galaxy0 | 21.05 | |
| Extracts QUAST metrics and generates FASTA files from JSON input. | 0.1.0+galaxy0 | 21.05 | |