svx-mdi-tools

The Michigan Data Interface (MDI) is a standardized framework for developing, installing and running HPC data analysis pipelines and interactive R Shiny visualization applications.

This svx-mdi-tools repository contains pipelines and apps for genome structural variant (SV) analysis by different library strategies from the Thomas Wilson laboratory at the University of Michigan.

Available tools

Pipelines and apps in stable release are:

• svCapture = find SVs in whole-genome capture sequencing (publication)

Pipelines and apps in beta, which have functioning code under development but no official releases yet, are:

• svWGS = find SVs in whole-genome sequencing data (without capture)
• svPore = find SVs in nanopore long-read whole-genome sequencing data
• scCNV = find CNVs in single-cell whole-genome amplification sequencing

Pipelines and apps in alpha, with exploratory code that is not considered stable:

• svAmplicon = find SVs in targeted amplicon sequences
• svDJ = analyze normal and aberrant V(D)J recombination events

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For more information about the MDI, please visit:

MDI Documentation MDI Basic Training MDI GitHub page

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