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The gig-map repository contains a set of tools to help understand what genes are shared
across a collection of microbial genomes. This wiki is intended to provide some useful guidance
for running the code contained in this software repository. It assumes a basic familiarity with
the command line and UNIX shell.
To use this workflow for the first time, you will need to first make sure that a set
of basic utilities are set up in your computational environment. The gig-map repository
uses Nextflow to coordinate a collection of workflows. The software
used at each step is distributed with Docker (or
Singularity) images.
Finally, the BASH Workbench is the
preferred method for configuring the launch of each individual workflow contained
within the repository.
Read Details on Getting Started
Want to get started analyzing your data? Follow this step-by-step guide to analyze your collection of genes and genomes.
The world of pan-genome analysis is rather complex, and gig-map only tackles a very
small part of this intellectual space. We invite you to read more about the scientific
background and motivation for the computational tools provided here:
Read Details on Scientific Background
Rather than providing a single stand-alone workflow, gig-map provides a small collection
of distinct tools which can be used together in different combinations. These include
utilities for downloading genes and genomes, deduplicating gene sequences, performing
sequence alignments, and generating interactive visualizations.
Read Details on Tool Inventory
