https://github.com/clinical-genomics/salty-reporter

A tool to convert JASEN analysis result files in JSON format to the same format as the microSALT reports. Initially used to figure out discrepancies between the tools.
https://github.com/clinical-genomics/salty-reporter

Last synced: 6 days ago
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A tool to convert JASEN analysis result files in JSON format to the same format as the microSALT reports. Initially used to figure out discrepancies between the tools.

• Host: GitHub
• URL: https://github.com/clinical-genomics/salty-reporter
• Owner: Clinical-Genomics
• License: gpl-3.0
• Created: 2023-08-11T14:40:49.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2024-03-12T14:10:47.000Z (10 months ago)
• Last Synced: 2024-03-13T12:57:45.765Z (9 months ago)
• Language: HTML
• Size: 86.9 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Salty Reporter

This is an experimental tool to generate reports similar to those from

[microSALT](https://github.com/Clinical-Genomics/microSALT), but based on the

analysis results from [JASEN](https://github.com/genomic-medicine-sweden/JASEN).

The aim is initially primarily to find out if there are any discrepancies

between the data from microSALT and JASEN, in order to guide the further work

on possibly replacing microSALT with JASEN for bacterial epityping.

It is not yet a MTP/Medicinal Technological Product. Whether it will be in the

future remains to see.

## Usage

1. Get the result file from running JASEN, for example the example output file

   `p1000_result.json`

2. Run salty reporter on the JASEN results like this:

   ```bash

   python saltyreporter/main.py -i  -o 

   ```