| Main use-cases | Multiplicity of Infection estimation |
| Authors | Samuel Assefa |
| Latest version | v1.03 |
| License | Not stated |
| Website | https://github.com/sammy-assefa/estMOI |
| Code repository | https://github.com/sammy-assefa/estMOI |
| Publication | https://academic.oup.com/bioinformatics/article/30/9/1292/235531 |
| Tutorial authors | Jody Phelan |
| Tutorial date | 11-Dec-23 |
estMOI
Summary sheet
Purpose
estMOI is a Perl script that estimates the MOI locally in the genome and then overall to obtain a global estimate. The inputs are alignment (BAM files), variant regions in the Variant Call Format/VCF and an optional file of regions to exclude from analysis. Minimal multiplicity is inferred by considering the maximum number of distinct haplotypes formed by combinations of a user-specified number of single nucleotide polymorphisms (SNPs) on single or paired reads.
Existing resources
- A manual can be found here
Citation
You can cite the tool using the following publication:
Assefa, Samuel A et al. “estMOI: estimating multiplicity of infection using parasite deep sequencing data.” Bioinformatics (Oxford, England) vol. 30,9 (2014): 1292-4. doi:10.1093/bioinformatics/btu005