This repository hosts vivaxGEN-Microhaps, an open-source pipeline designed for processing targeted amplicon sequencing data. It offers two distinct sub-pipelines:
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Microhaplotype Calling: This sub-pipeline, adapted from the malaria-amplicon-pipeline and converted to use Snakemake, generates microhaplotype allele tables.
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SNP-based Variant Calling: Leveraging the vivaxGEN NGS-Pipeline, this sub-pipeline generates standard VCF files for SNP analysis.
The main documentation, which cover complete installation and tutorials, is here.
Note for Conda-based users! Be sure you are not in a conda environment or in the (base) conda environment prior to installing. To deactivate your conda environment or (base) environment, enter:
conda deactivate
Install the pipeline with the following command (note: must be run under relatively current version of bash):
"${SHELL}" <(curl -L https://raw.githubusercontent.com/vivaxgen/MicroHaps/main/install.sh)
The installation requires ~ 20-45 minutes as most of R packages need to be recompiled during installation.
Once the installation finished, it will show the command to activate the pipeline, such as:
/path/to/vvg-MicroHaps/bin/activate
This activation command has to be executed before all commands of the pipeline can be run. When activated, the terminal will show the (µhaps) prompt.
The installation process also performs indexing of the reference files. However, in case that the indexing fails, please perform manual indexeing using the command:
ngs-pl initialize --target wgs
To test your install, and read about programme specifications / options:
ngs-pl run-microhaplotype-caller --help
To update the pipeline line, assuming that the environment has been activated, run the following command:
$VVGBIN/update-box
