Rainbow Semi-Automated Workflow

Rainbow is a scalable workflow for whole genome sequencing analysis. It combines:

1. PICARD, a Java-based command-line utility that manipulates SAM/BAM files
2. Bowtie, an ultrafast and memory efficient short read aligner
3. SoapSNP, an accurate genotyper
4. SNP_Merger, an in-house developed application for SNP consolidations

These tools are combined in Semi-automatic, parallel pipeline that runs in the cloud (Amazon Web Services’ EC2, S3, and Elastic MapReduce offerings in this case).

Index

• Prerequisites
• Using the AMI
• Using the Configuration Script
• Detailed Prerequisite Instructions
• Installation and Run
• Results
• TimeAndCost

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