FunVIP 0.5.4

Fungal Validation & Identification Pipeline

FunVIP

FunVIP is now published please cite:

Seo CW, Yoo S, Cho Y, Kim JS, Steinegger M, Lim YW. FunVIP: Fungal Validation and Identification Pipeline based on phylogenetic analysis. J. Microbiol. 2025;63(4):e2411017.

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 multiple genetic marker
• Database sequence validation algorithm implemented

Bug reports are always welcomed

IMPORTANT NOTICE: The python dependency for Linux platform has changed from 3.12 to 3.11 for TCS inclusion. Please remake conda environment for FunVIP 0.3.25 update

Tutorial

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

Documentation

• See Documentation for advanced usage !
  
  

Requirements

• Conda or Mamba environment

* See here for how to install conda environment

* Recently, Mamba is a lot faster than conda. See here to how to install mamba 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

• Example output tree of FunVIP

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