DREPAL-IPCINGSTOOLKIT

DREPAL-IPCINGSTOOLKIT (/DREPAL-IPCINGSTOOLKIT/) is an developed within the framework of the ‘DREPAL’ project carried out by the Parasitology Departement of institut Pasteur of Ivory Coast (IPCI) for the analysis of NGS data. It is a software toolbox composed of stand-alone options or organized as a pipepline for quality control, which remains a crucial step in various downstream analyses. The dection of SNP (Simple Nucleotide Polymorphism), INDELs (INSERTION / Deletion) mutations and the elaboration of mutation matrix carried by several samples. Check out the usage section for further information, including how to installation the project.

Note

This project is under active development.

Contents

• Installation
  • Download and Installation of Outbuildings
    • System requirements
    • Setup process
    • Starting the streamlit server
    • In your web browser
  • Deploy DREPAL-IPCINGSTOOLSKIT for many users
• Usage
  • Account creation
    • Login Screen
  • PRESENTATION OF THE DIFFERENT PANELS
• Left Panel
  • Use of disk ressources
  • Operations menu
• Main Panel
  • Sequence Import
    • Clinical Isolates (fastq,gz)
      • Method 1
      • Method 2
      • Method 3
    • References Import (fasta files)
  • Quality Controle
    • Visualisation
    • Trimming
  • Reference Indexed
  • Host Substract
  • Pathogen Extraction
  • Variant Calling
  • Mutation Matrix
  • Variant Annotation
  • Directory Management
  • Doudle Digital Soustraction
• Bibliography