Cobalt

Rationale

Cobalt, the color-space Bayesian variant calling tool, is a next-generation sequencing tool for variant calling specifically designed for the Applied Biosystems SOLiD sequencer output. At the heart of Cobalt lies a probabilistic model carefully designed to take advantage of SOLiD reads’ encoding as color-space sequences to detect and distinguish both mutations from a reference genome and sequencing errors occurring in the various reads. This enables Cobalt to have good precision-recall curves, even in low-coverage situations, while keeping a low memory footprint and fast running time.

Implementation

Cobalt is implemented in C and provides user-friendly Ruby scripts. The source is available here.