MARTi
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Introduction
Installation
Installation overview
Installation by hand
Installation with bioconda
Using the MARTi Docker image
Job schedulers
Database Installation
Using MARTi
Running MARTi
Starting analysis
The MARTi GUI
Config file format
Advanced features
FAQs
Example and tutorial
Change history
MARTi
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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
Installation with bioconda
Install Mamba
Channel configuration
Install MARTi
Using the MARTi Docker image
Test data
Persistent options file
GUI only
Job schedulers
Database Installation
Pre-built Blast databases
Custom databases
CARD
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
The Samples page
The Dashboard page
The Compare page
New analysis page
Options
Taxonomic ranks
Config file format
Sample and global settings
Pre-filtering settings
LCA classification settings
BLAST processes
Centrifuge processes
Kraken2 processes
Metadata
Example
Advanced features
Re-running analysis without running BLAST
FAQs
Why does the taxa accumulation curves go down as well as up?
How can leaf nodes have more reads below the node?
Example and tutorial
Engine-initiated local analysis
Docker - GUI-initiated local analysis
Change history
Version 0.9.15 (Coming soon)
Version 0.9.14 (16 Jun 2023)
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