mbctools

This crossplatform (Linux, OSX, Windows) Python program is a toolkit to make the use of VSEARCH easier and interactive, helping to analyze your Metabarcoding NGS data in best conditions. It features the following MAIN MENU:

1 -> INITIAL ANALYSIS (mandatory): read merging, sample-level dereplication, sequence clustering,
	chimera detection, affiliation of sequences to loci, and sequence re-orientation

2 -> PRIMER REMOVAL AND SELECTION OF MINIMUM SEQUENCE ABUNDANCE LEVELS ACCORDING TO USER-DEFINED THRESHOLDS

3 -> GENERATION OF A UNIQUE SEQUENCE FILE FOR EACH LOCUS (comprising all samples' data)

4 -> EXPORTING ANALYSIS RESULTS INTO metaXplor FORMAT

mbctools reference:

Christian Barnabé†, Guilhem Sempéré†, Vincent Manzanilla, Joel Moo Millan, Antoine Amblard-Rambert and Etienne Waleckx (†Co–first authors). mbctools: A User-Friendly Metabarcoding and Cross-Platform Pipeline for Analyzing Multiple Amplicon Sequencing Data across a Large Diversity of Organisms. bioRxiv doi: https://doi.org/10.1101/2024.02.08.579441

VSEARCH reference:

Rognes T, Flouri T, Nichols B, Quince C, Mahe F (2016). VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584 doi: 10.7717/peerj.2584 https://doi.org/10.7717/peerj.2584

metaXplor reference:

Guilhem Sempéré, Adrien Pétel, Magsen Abbé, Pierre Lefeuvre, Philippe Roumagnac, Frédéric Mahé, Gaël Baurens, Denis Filloux. metaXplor: an interactive viral and microbial metagenomic data manager. GigaScience, Volume 10, Issue 2, February 2021, giab001, https://doi.org/10.1093/gigascience/giab001

Requirements

• Python v3.7 or higher
• VSEARCH v2.19.0 or higher must be installed and accessible in the PATH (binaries for all platforms available at https://github.com/torognes/vsearch, along with installation procedure descriptions)
• Windows users will need to enable Powershell script execution using the Set-ExecutionPolicy command

Procedure for Windows setup:

• Download and install latest Python3 release from https://www.python.org/downloads/ (simplest way is to use the 64-bit installer). Don't forget to tick the "Add python.exe to PATH" checkbox before launching setup

• Download and unzip latest VSEARCH release from https://github.com/torognes/vsearch/releases

• Locate the path to the vsearch.exe executable (e.g., C:\Users<UserName>\Downloads\vsearch-2.28.1-win-x86_64) and add it to the PATH environment variable as follows:

  • Press Win + R, type sysdm.cpl, and press Enter
  • In the Advanced system settings tab, click Environment Variables
  • Find the Path environment variable and select it. Click Edit
  • In the Edit System Variable window, add an entry pointing to the location of vsearch.exe (not including the file name, only its full path). Click OK until all windows disappear

• Open a command prompt and type "pip install mbctools"

You should then be able to launch mbctools directly from the command prompt or Powershell, by typing "mbctools".