The purpose of this repository is to introduce researchers in Neafsey Lab in the analysis of genotyping information generated through amplicon sequencing (also called Microhaplotype genotyping).
This covers 8 tutorials:
An example of a customized analysis of the AMPLseq data for Plasmodium falciparum, and
PvGTSeq data for Plasmodium vivax.
Our GitHub repository contains a set of functions that allows the
user to upload and manipulate the genotypic information stored in .tsv
tables (in CIGAR format) that has been generated by the malaria-amplicon-pipeline
of our lab. All those functions and the required libraries are in the R
scripts amplseq_functions.R
and amplseq_required_libraries.R,
and an additional set of Rcpp functions for the estimation of IBD and
eigenvectors are in the files hmmloglikelihood.cpp
and Rcpp_functions.cpp.
Some of the functions require additional input files such as fasta files
for reference strains or tables of alleles associated with drug
resistance. These additional information is stored in the folder doc/reference.
The AMPLseq
and PvGTSeq
tutorials have been created to introduce the final users to all the set
of functions in this repository, while the Intro
to MHap-Analysis pipeline tutorial shows how to generate automated
reports. To run these tutorials data sets are stored in the folder doc/data.
The samples for these tutorials comes from a collaboration with the
groups of Caucaseco in Colombia, Stella Chenet in Peru, and David Forero
in Venezuela.