FunVIP

Fungal Validation & Identification Pipeline

An automatic tree-based sequence identification and validation pipeline for fungal (or maybe other) species

• Automatic tree-based identification
• Works with multigene
• Data validation algorithm implemented

This is Beta release. Bug reports are welcomed

Tutorial

• Part 1 - Getting started!
• Part 2 - Preparing database and query
• Advacned tips
  
  

Documentation

• See Documentation for advanced usage !
  
  

Requirements

• Conda environment

* See https://www.anaconda.com/products/individual for how to install conda environment

Installation

• Windows
• Mac - apple silicon
• Linux
• from source
  
  

Usage

FunVIP --db {Your database file} --query {Your query file} --email {Your email} --gene {Your genes} --preset {fast or accurate}

Example

FunVIP --db Penicillium.xlsx --query Query.xlsx --email {Your email} --thread 8 --gene ITS BenA RPB2 CaM --preset fast

* See documentation for detailed usage

How to make database?

See example database here

Results

• Section Assignment.xlsx : Your clustering result is here. You can find which of your sequences are clustered to which section
• Identification_result.xlsx : Your final identification result. Shows how your sequences were assigned to species level through tree-based identification
• report.xlsx : overall statistics about the tree. If your find taxon ends with numbers, these taxon are found to be paraphyletic, so should be checked
• /Tree/{section}_{gene}.svg : Final collapsed tree in svg format. Can be edited in vector graphics programs, or in powerpoint (by ungroup)
• /Tree/{section}_{gene}_original.svg : Uncollapsed tree for inspection

Scheduling

1. Beta release part 1 (2023 Feburary ~ As paper published, ver 0.3) Will be tested by our lab memebers to fix bugs and advance features
2. Beta release part 2 (As paper published ~ When pipeline gets stabled, ver 0.4) Will be tested by peer taxonomists
3. Stable release (ver 1.0)

License

GPL 3.0