Methods

This page summarizes the methods available from the Comai lab

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TILLING and High throughput sequencing

• Illumina library construction with amplicons, or any input DNA
• Bioinformatics pipeline for mutation discovery

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Custom barcoding for Illumina and Illumina barcoded reads pipeline

• Barcoded Data Preparation Tools
• Custom barcoded Illumina adapters
  • Strategy and Explanation
  • Barcode generator, a python program
  • 96 tested 5-letter barcodes in Illumina PE adapters

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Genotyping and Mutation Discovery

• a Genotyping by Sequencing method
• BWA-DoAll, a package for batch library processing and alignment
• Tools for Mpileup generation and parsing
• MAPS: a Mutation Detection and Genotyping tool

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Exome capture: genotyping and mutation discovery

• MAPS: a Mutation Detection and Genotyping tool

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Discover CNV in genome (a Matt Porter and Korf lab collaboration)

• DupHMM, a fast program to detect copy number variants from SAM files

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Funding

This page and the connected tools are funded by:

• NSF Plant Genome grant DBI-0733857 (Functional Genomics of Polyploids)
• NSF Plant Genome grant DBI-0924025. Heterosis Challenge Grant (HCG):The Regulatory Disruption Hypothesis for Heterosis
• NSF Plant Genome grant DBI-0822383 (“TILLING by Sequencing”)
• National Institutes of Health R01 GM076103-01A1 (Dosage dependent regulation in hybridization) to LC.