mad4hatter-tools

Utility scripts for working with mad4hatter pipeline outputs.

Contents

convert_outputs/

Scripts to convert mad4hatter results from older releases to v1.0.0 format. Supported input versions: v0.1.8, v0.1.9, v0.2.0, v0.2.1, v0.2.2. Releases prior to v0.1.8 are not supported.

See convert_outputs/CONVERSION_NOTES.md for a full description of column mappings, files that are renamed or reorganized, and fields that cannot be recovered from older outputs.

Files

• run_convert_mad4hatter.R — main script to edit and run. Set your input/output paths here and source the functions file.
• convert_mad4hatter_functions.R — all conversion functions. Do not need to edit this.
• inputs/ — reference files required by the converter:
  • target_id_conversion_table.tsv — maps old locus names to new target_name and pool
  • amplicon_info.tsv — amplicon panel information for panel_information/ output
  • references.fasta — reference sequences for panel_information/ output
  • principal_resistance_marker_info_table.tsv — resistance marker reference for panel_information/ output

Usage

Edit run_convert_mad4hatter.R with your paths and run it from RStudio or the R console. Requires the tidyverse package.

Issues

If you encounter problems or results from an unsupported version, please submit an issue.