Welcome to HaploCoV’s documentation!

HaploCoV: provides a collection of Perl utilities that can be used to:

1. align complete assemblies of SARS-CoV-2 genomes with the reference genomic sequence and identify genomic variants,

2. pinpoint regional variation and flag genomic variant with “increased frequency” locally or globally,

3. identify epidemiologically relevant variants and/or novel lineages/sub-lineages of the virus (using a custom scoring system),

4. extend an existing classification system to include novel designations/variants,

5. and to classify one or more genomes according to the method described in Chiara et al 2021 https://doi.org/10.1093/molbev/msab049 and/or any other classification system of your choice.

HaploCoV is composed of 9(+3) utilities, which are combined in a workflow. The complete workflow can be executed with just a couple of commands (or several commands for more complex use cases). In brief, input files need to be formatted according to the format used by HaploCoV by applying either addToTable.pl or NexstainToHaploCoV.pl (depending on the input, see below). Then the complete HaploCoV workflow can be executed by running HaploCoV.pl (recommended) or, if you prefer, by running each individual tool in the HaploCoV workflow in the right order yourself. Please see the manual for point to point instructions and tips for the execution of HaploCov.

Should you find any of this software useful for your work, please cite: Chiara M, Horner DS, Gissi C, Pesole G. Comparative genomics reveals early emergence and biased spatio-temporal distribution of SARS-CoV-2. Mol Biol Evol. 2021 Feb 19:msab049. doi: 10.1093/molbev/msab049.

If you find any issue with the software, please contact me, or report it on github.

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?

Indices and tables

• Index

• Module Index

• Search Page