Topics

• Welcome
  • Introduction
  • About the COHESIVE Project
  • Quick start
  • Features
    • Main
    • Tables
    • Data Import/Export
• Main objects
  • Samples
  • Aliases
  • Metadata
  • Exams
• Filter samples
  • Tags
    • Introduction
    • Manage Tags
  • Cart
    • Introduction
    • Manage Cart
    • Activate Cart
• Analyses
  • Run analyses
  • Run analysis steps
  • Check analyses
  • Tool Descriptions
    • Introduction
    • Tools for Long Reads
    • Single sample
      • 1 Pre-processing
        • 1PP_trimming
        • 1PP_hostdepl
        • 1PP_filtering
        • 1PP_downsampling
        • 1PP_generated
      • 2 Assembly
        • 2AS_denovo
        • 2AS_mapping
      • 2 Metagenomics
        • 2MG_denovo
      • 3 Taxonomy
        • 3TX_class
        • 3TX_species
      • 4 Genome annotation
        • 4AN_AMR
        • 4AN_genes
      • 4 in silico typing
        • 4TY_cgMLST
        • 4TY_lineage
        • 4TY_flaA
        • 4TY_MLST
        • 4TY_wgMLST
    • Multi sample
      • SNP-based clustering
        • CFSAN
        • kSNP3
        • VCF2MST
      • Pangenome extraction
        • Snippy-core
        • Panaroo
      • Gene-by-gene based clustering
        • GrapeTree
        • Reportree
    • Pipelines
      • Mapping Segmented Viruses
      • Covid Emergency
      • Depletion and de novo
      • Genome draft
      • Enterotoxin S. aureus finder
      • NgsManager
      • Raw Reads Processing
      • Typing on Bacteria
      • WNV - Lineage Calculation and Mapping
      • Filtering and de novo
• Reports
  • Reports
• Downloads
  • Download Procedure
  • Download for Windows Users
• Upload
  • Introduction
  • Upload Functionalities
    • Upload from NCBI
    • Manual Upload
  • Prepare Upload
  • Check Upload
  • Zip and Metadata Rules
• Administration
  • Authentication Rules
• Dashboards
  • SPREAD (GrapeTree)
  • Auspice
• FAQs
• News
• Resources
  • Keyboard shortcuts
  • Videos