PAINT: Leishmania Sexual Reproductive Strategies As Resolved Through Compuational Methods Designed for Aneuploid Genomes

Jahangheer S. Shaik, Deborah E. Dobson, David L. Sacks and Stephen M. Beverley

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SYSTEM REQUIREMENTS

AGELESS Package

Example Data

Generate Ploidy Matrix

This utility finds the chromosomal somies in each sample. Assumes all the samples are diploid.

Prerequisites

1) Align the fastq files to the reference genome of interest using your favourite aligner (Bowtie, BWA, Novoalign etc.)
2) Sort the generated Binary alignment map (BAM) file using samtools 'sort' function
3) Generate an coverage files using findReadDepth utility of PAINT. Place all the coverage files in one directory

How to Run it?

The ConcatenatedPloidyMatrix utility of PAINT package takes coverage files generated using findReadDepth utility of PAINT and determines the somies. Type java -jar PAINT.jar ConcatenatedPloidyMatrix utility -h for options.

-i is the directory where all the coverage files are placed. -o is the output file name.

Command Example

java -jar PAINT.jar ConcatenatedPloidyMatrix -i "..\DemoData\readDepth\" -o "..\DemoData\otherFiles\concatPloidyMatrix.txt"

Output

The output of the listAlleles program looks as follows:

Here the chromosomes are in columns and samples are in rows. All the samples are assumed to be diploid when determining the somies. If the samples are of other ploidy, multiply all the somies of that sample by its ploidy and divide by 2.