Skip to main content

Table 1 The advantages and limitations of bioinformatics tools current available for analysis of polyclonal infections and estimation of MOI

From: Molecular approaches to determine the multiplicity of Plasmodium infections

Software/approach Implementation Data source Advantage Limitation References
Fws Fws statistics SNPs Provide a summary statistic of relative inbreeding and correlation with MOI Does not provide a direct estimate of COI Manske et al. [108]
estMOI Perl scripts  TDS estimate MOI, SNP combinations and proportion in a specific genomic region Partial genomic region, sufficient density of SNPs in an amplicon is required Assefa et al. [107]
COIL Perl scripts web interface SNPs Use genome-wide SNPs to infer the number of strains and their proportions Does not infer haplotypes; sequence read counts are assumed to be unbiased and the SNPs are unlinked Galinsky et al. [93]
SeekDeep Perl scripts TDS No reference sequence required, direct estimation of amplicon haplotype cluster and frequency Partial genomic region, threshold for haplotype cluster calls needs to be determined by empirical methods in each study Hathaway et al. [104]
HaplotypR R package TDS Direct estimation of haplotype cluster and frequency based quality filtering of sequencing reads Partial genomic region, enough high polymorphism in the amplicon is required and unable to deal with indel of amplicon Lerch et al. [102]
pfmix R package SNPs Infer inbreeding coefficients using WGS to assess within-sample parasite infections Does not infer haplotypes, sequence read counts are assumed to be unbiased and SNPs need to be unlinked O’Brien et al. [110]
THE REAL McCOIL Perl scripts web interface SNPs Infer the number of strains and their proportions Does not infer haplotypes, sequence read counts are assumed to be unbiased and SNPs need to be unlinked Chang et al. [94]
DEploid R package SNPs Estimate the number of strains, their relative proportions, and the haplotypes Reference panel required, more reference strains are better. Multiallelic variant not considered Zhu et al. [111]
  1. SNPs single nucleotide polymorphism, TDS targeted deep sequencing, WGS whole genome sequencing, MOI multiplicity of infection