Contrail

Contrail assembles large genomes from short-read second-generation sequencing data using Hadoop-based distributed computing to enable scalable de novo genome assembly in cloud environments.

Key Features:

• Hadoop-Based Infrastructure: Utilizes Hadoop for scalable distributed processing of large sequencing datasets.
• Cloud Compatibility: Operates in cloud environments to scale compute and storage for large-scale genome assembly.
• Short-Read Assembly: Specializes in assembling genomes from short-read data produced by second-generation sequencing technologies.

Scientific Applications:

• De novo assembly of large genomes: Produces genome assemblies from short reads for organisms with large or complex genomes.
• Genomic research on genetic diversity, evolution, and complex traits: Supports studies in genetic diversity, evolutionary biology, and complex trait analysis by providing assembled genomes from short-read data.

Methodology:

Processes different types of data produced by second-generation sequencers and accommodates changes in read lengths and sequencing technologies; incorporates assembly algorithms tailored for short-read assembly to address sequence coverage and error rates; uses Hadoop-based distributed computing in cloud environments to manage and process large datasets; and provides recommendations on sequencing strategies to enable high-quality genome assemblies.