MIPTools Documentation
Welcome to the MIPTools User Guide!
MIPTools is a suite of computational tools that are used for molecular inversion probe (MIP) design, data processing, and analysis. Throughout much of this tutorial, we assume a user interested in using MIPs as a cost effective way to amplify and sequence hundreds to thousands of targeted regions of the genomes from hundreds to thousands of pooled barcoded samples. Our group primarily uses these MIPs for genomic surveillance of Plasmodium falciparum targets, but we have attempted to generalize this tool for other questions and datasets. This toolset also assumes the use of unique molecular identifiers (UMIs) which tell us how much of each type of DNA was originally present in each sample (prior to PCR amplification).
- A typical pipeline might look something like this:
First, a user might design MIP probes (using the probe design tool of this program) that have UMIs added to each MIP probe.
Second, a user might perform mip capturing reactions, PCR, sample barcoding, and illumina sequencing. The output data should be demultiplexed, resulting in two fastq files per sample. Bench techniques for these experiments are described elsewhere.
Third, the data is wrangled to generate an output file describing which genotypes (or haplotypes) are found at which abundances in each sample for each targeted region, using:
a sample sheet that describes the samples
a fastq folder of samples
a project resources folder that describes the probes
Finally, the haplotype data is analyzed using a variant caller (Freebayes is currently our best-supported tool) to produce a VCF file and some output tables with frequencies and prevalences of mutations of interest, using:
a sample sheet that describes the samples
a folder containing the wrangled haplotype data
a folder of indexed genomes for your species of interest
a project resources folder that describes the probes
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