AGELESSMolecularMicro

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

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




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SYSTEM REQUIREMENTS

PAINT Package  

Example Data

Generate BAM file that contains reads indicative of regions that are conserved across both the species

PipelinePipelineInterspecies

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) If the two genomes corresponding to two species being studied have high synteny, use FindCommonSpecificReadsChrWise  utility else use FindCommonSpecificReads of PAINT. The reads alinged to both genomes are inputs to other utilities in PAINT