Start here

• Introduction
  • Overview
  • Local analysis configuration
  • HPC configuration
  • Inside MARTi Engine

Installation

• Installation overview
• Installation by hand
  • Overview
  • Prerequisites
  • Downloading
  • MARTi Engine (back-end) installation
  • MARTi GUI (front-end) installation
  • marti_engine_options.txt
  • Possible macOS differences
• Installation with bioconda
  • Install Mamba
  • Channel configuration
  • Install MARTi
• Job schedulers
  • Notes about SLURM
  • Local vs SLURM
• Reference Databases
  • Pre-built Blast databases
  • Custom Blast databases
  • CARD
  • Kraken2 Databases
  • Centrifuge Databases

Using MARTi

• Running MARTi
  • Key concept
  • Initiating analyses in the local configuration
  • Initiating analyses in the HPC configuration
  • rsync’ing or mapping?
  • Connecting a Mk1C in a local configuration
• Starting analysis
  • Starting MARTi from the command line
  • Creating a config file
  • Blast process configuration
• The MARTi GUI
  • Launching the GUI
  • The Samples page
  • The Dashboard page
  • The Compare page
  • New analysis page
  • Options
  • Taxonomic ranks
  • Projects
• Config file format
  • Sample and global settings
  • Pre-filtering settings
  • LCA classification settings
  • BLAST processes
  • Diamond processes
  • Centrifuge processes
  • Kraken2 processes
  • AMR Walkout
  • Metadata
  • Example
  • Processing Barcodes Example
• Continuing after errors
  • Restarting the MARTi Engine
  • Forcing the MARTi Engine to start from the beginning
  • Re-running the analysis without re-running BLAST
• Advanced features
  • Re-running analysis without running BLAST
• Downstream analysis
  • Through the GUI
  • BLAST files
  • The lcaparse directory
  • The megan directory
• Example and tutorial
  • Engine-initiated local analysis
  • GUI-initiated local analysis
• Change history
  • Version 0.9.33 (11 June 2026)
  • Version 0.9.31 (7 Nov 2025)
  • Version 0.9.30 (19 Oct 2025)
  • Version 0.9.29 (5 Seo 2025)
  • Version 0.9.27 (9 Jul 2025)
  • Version 0.9.26 (30 Jun 2025)
  • Version 0.9.25 (25 Jun 2025)
  • Version 0.9.23 (19 Feb 2025)
  • Version 0.9.22 (16 Feb 2025)
  • Version 0.9.20 (23 Jan 2025)
  • Version 0.9.18 (17 Oct 2024)
  • Version 0.9.16 (1 Mar 2024)
  • Version 0.9.15 (30 Nov 2023)
  • Version 0.9.14 (16 Jun 2023)

Troubleshooting

• Engine problems
  • Troubleshooting principles
  • BLAST problems
  • Java heap problems
• GUI problems
• FAQs
  • Why does the taxa accumulation curves go down as well as up?
  • How can leaf nodes have more reads below the node?
  • Why do AMR hits on the heatmap sum to over 100% when grouped by “Drug class”?
  • What are the “Other” and “Higher Taxa” categories for?
  • Can I use TaxaFilter for Kraken2?
  • What is the LCA minimum abundance cutoff?