Introduction

Cosigt (Pronunciation: /koˈziː.d͡ʒi.ti/) pipeline is an end-to-end workflow whose aim is to assign structural haplotypes to sequenced samples using pangenome graphs.

Contents

1. Setup - Initial pipeline configuration and installation instructions
   • → Go to Setup Guide
2. Workflow - Broad explanation of the workflow principles
   • → Go to Workflow Guide
3. Use Cases - Examples using publicly available data to demonstrate pipeline setup, input preparation and workflow functionality
   • → Go to Use Cases

Citation

Refer to this manuscript if you are using our pipeline in your work:

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An initial application of cosigt workflow is also presented in this (opens new window) manuscript:

Bolognini, D., Halgren, A., Lou, R.N. et al. Recurrent evolution and selection shape structural diversity at the amylase locus. Nature 634, 617–625 (2024).