URL: http://pathogenseq.lshtm.ac.uk/estmoi
Proper Citation: estMOI (RRID:SCR_006192)
Description: A per-based software 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. It 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. # Short reads are aligned to a reference genome using BWA, BOWTIE, SMALT or other short read aligners to generate a BAM file. # Single Nucleotide Polymorphisms (SNPs) are then identified using SAMTools/BCFtools and stored in the VCF format. # 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).
Abbreviations: estMOI
Synonyms: estMOI - Estimating multiplicity of infection using parasite deep sequencing data
Resource Type: software resource
Defining Citation: PMID:24443379
Keywords: multiplicity of infection, parasite, genome, high throughput sequencing, single nucleotide polymorphism, chromosome
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