Trans-ABySS

Trans-ABySS assembles short-read transcriptome data de novo by performing multiple assemblies under varying stringency levels and merging contigs to support transcript discovery and analysis.

Key Features:

• De novo short-read assembly: Performs de novo assembly of short-read RNA-seq data to reconstruct transcript contigs.
• Variable-stringency assembly: Assembles read substrings under varying stringency levels to accommodate local read density variation.
• Contig merging: Merges resulting contigs from multiple assemblies to improve assembly accuracy.
• Scalability: Scales to large sequencing datasets, demonstrated on 7.4 gigabases of 50-base-pair paired-end Illumina reads.
• Sensitivity and specificity: Enables sensitive and specific detection of known, novel, and alternative transcript structures.
• Adaptive read-density handling: Manages variations in local read densities to achieve comprehensive coverage.
• Performance vs reference-based methods: Shows superior performance in detecting expressed transcripts compared to traditional reference-based assembly methods.

Scientific Applications:

• Transcript discovery: Identification of known, novel, and alternative transcript structures from RNA-seq data.
• Gene expression analysis: Reconstruction of transcripts to support downstream gene expression quantification and analysis.
• Transcriptomic variation studies: Characterization of alternative splicing and transcriptomic variation in biological samples.
• Empirical demonstration: Applied to poly(A) RNA from adult mouse liver using 50-base-pair paired-end Illumina reads (7.4 gigabases) to demonstrate capability.

Methodology:

Assembles read substrings under varying stringency levels and merges the resulting contigs.