Reporting Module

We provide a script that generates a PDF report for each el_gato run using the report.json file located in the output folder for each sample. You can generate reports for one or more samples, including assembly, and review the results.

• Dependencies
• Usage
  • Quickstart
  • All available arguments
• Report summary
  • Example image of pdf report

Dependencies

• fpdf2

Usage

Quickstart

elgato_report.py -i <path/to/report1.json> [<path/to/report2.json> ...] -o <path/to/output/report.pdf>

All available arguments

Usage information printed when running elgato_report.py with -h or --help

options:
  -h, --help            show this help message and exit
  -i, --input_jsons     path to one or more report.json files
  -o, --out_report      desired output pdf file path
  -s, --shorten_names   shorten long sample and contig names to prevent line wrapping
  -n, --no_header       Do not include the header in the report
  -d,  --disclaimer     Include disclaimer in footer
  --custom_header       Provide a custom header as a string in your command
  --header_file         Provide a custom header in a text file

Report summary overview

A description of the sections that are generated when using the el_gato reporting module, which if reads were used you get the Paired-end Reads subsection and if you used assemblies then the Assembly subsection will be included. In the example image below, the report summary page is shown.

• Report Summary page: Summary of el_gato and complete ST profile for each sample included in the report.

• Definitions Overview page: ST definitions key and evidence for support of mompS allele call key.

• Paired-end reads: Locus coverage information and mompS primer information parsed by each sample.

• Assembly: BLAST hit length and sequence identity thresholds and locus location information parsed by each sample.

Example image of pdf report

Figure 1: Example report -This report was generated using the elgato_report.py script and only shows the first summary page of the report.