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.
All tutorials are here.