SATRAP

SATRAP converts assembled SOLiD color-space DNA sequences into base-space to enable accurate de novo assembly and analysis of genomes and transcriptomes in RNA-seq workflows.

Key Features:

• Color-space to base-space conversion: Converts assembled SOLiD color-space sequences into base-space sequences for downstream analysis.
• Error propagation mitigation: Mitigates propagation of translation errors that can cause cascading inaccuracies in color-space to base-space translation.
• De novo assembly support: Produces base-space output suitable for de novo assembly of genomes and transcriptomes.
• Modularity and pipeline integration: Provides a modular design intended for integration into RNA-seq analysis pipelines.
• Compatibility with Oases: Designed to be compatible with the Oases de novo transcriptome assembler.
• Validation on transcriptomic data: Tested and validated using both simulated and real transcriptomic datasets.

Scientific Applications:

• De novo genome assembly: Enables use of SOLiD sequencing data in de novo genome assembly pipelines by supplying base-space sequences.
• De novo transcriptome assembly: Enables de novo transcriptome reconstruction from SOLiD-derived assemblies in RNA-seq workflows.
• SOLiD data integration: Facilitates incorporation of SOLiD color-space sequencing data into standard base-space analysis workflows.

Methodology:

Conversion of assembled SOLiD color-space sequences into base-space; validated on simulated and real transcriptomic datasets; designed for modular integration with de novo assemblers such as Oases.