estMOI

estMOI is intended to estimate Multiplicity of Infection (MOI) in parasite genomic sequence data. It is primarily developed to address the limitations of current laboratory (PCR) based estimates of multiplicity using high throughput sequence data as follows:

INPUT files: estMOI requires a BAM (alignment output of short reads to the reference genome), VCF (a file with information on variant calls) and FASTA (reference genome) files.
1. Short reads are aligned to a reference genome using BWA, BOWTIE, SMALT or other short read aligners to generate a BAM file.
2. Single Nucleotide Polymorphysms (SNPs) are then identified using SAMTools in the VCF format.
3. The reference FASTA file is expected to be indexed using 'samtools faidx' to generate a *.fai file.

estMOI generates files containing MOI estimates for each SNP combinations (file with name *.LOG) and a summary for all chromosomes (file with name *.txt).

Contact: samuel.assefa @ lshtm.ac.uk