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

Index
Edit on GitHub

Index

© Copyright 2022, Matteo Chiara. Revision a4b4514e.

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