Methods and Data

This page summarizes the methods and data available from the Comai lab

---

TILLING and High throughput sequencing

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

---

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

---

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

---

Exome capture: genotyping and mutation discovery

• MAPS: a Mutation Detection and Genotyping tool

---

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

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

---

Heterosis

• RNAseq reads from rice varieties and hybrids
• CHIPseq reads from rice varieties and hybrids

---

Polyploidy

• RIL map of the Col-0 x Warschau population
• Arabidopsis arenosa genomic information
  • Genomic contigs
  • cDNA contigs
• Karyotypes of trisomic and translocated trisomic. [1] Dataset
• Bin-by-sam, a karyotyping tool
  • Detailed run directions and examples can be found here.

---

Functional genomics of plant polyploids: NSF DBI 0733857

• ABC data page

---

Protein Family Data Files

• Pfam data page

---

REVOLUTA legacy data

• The REV page

---

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.