HaploCoV
latest

HaploCoV in brief

  • Things HaploCoV can do

Data and formats

  • Where do I get the data
  • Reference genome
  • Genomes and metadata
  • GISAID
  • GISAID-Augur
  • Required metadata
  • Nextstrain
  • Important: providing “custom” data

Prerequisites

  • Perl and mummer
  • Mummer installation
  • Unix, ubuntu
  • Unix, from binaries
  • Mummer installation MacOS X
  • Configuration files

HaploCoV: input

  • HaploCoV format and input
  • HaploCoV format for metadata
  • Dates and time in HaploCoV
  • Geography and places
  • Formatting the input
  • GISAID data: addToTable.pl
  • NextStrain data: NextStrainToHaploCoV.pl
  • Genomic variants file
  • Pre computed genomic variants files
  • Designations files in HaploCoV
  • Novel designations
  • Computational resources

HaploCov: workflow

  • For impatient people
  • HaploCoV.pl
  • Configuration (Locales file)
  • Output (and intermediate files folder)
  • Genomic variants files (Configuration II)
  • Locales: special/reserved keywords
  • Parameters file (configuration III)
  • Designations file
  • Intermediate files and what to make of them
  • How to interpret HaploCoV’s results
  • Header and sections
  • Scores and novel genomic variants
  • Prevalence

HaploCoV: tools

  • For impatient people
  • 2 Compute high frequency genomic variants
  • 3 Derive novel groups
  • 4 Compute genomic features of SARS-CoV-2 lineages and sublineages
  • 5 Prioritization of novel groups/lineages
  • 6 Assign genomes to new groups
  • 7 Prevalence report

HaploCoV: Use Cases

  • Use Cases
  • Use case 1. Alpha
  • Use case 2. Delta
  • Use case 3. Omicron
  • What to do next

HaploCoV: advanced

  • Subsetting data
  • Geographically restricted analyses: how to analyse a specific Area, Country or region of interest
  • Select a specific lineage/HG
  • Select by time
  • Can I combine all of the above?
HaploCoV
  • Search

© Copyright 2022, Matteo Chiara. Revision a4b4514e.

Built with Sphinx using a theme provided by Read the Docs.