Oases

Oases assembles transcriptomes from short-read RNA-seq data to reconstruct transcript isoforms and represent alternative splicing and expression variation.

Key Features:

• De Novo Assembly: Constructs transcripts from short-read sequencing technologies without relying on a pre-existing genome.
• Isoform Resolution: Handles alternative splicing events to represent multiple transcript variants.
• Expression Range Handling: Manages a broad spectrum of expression values across experimental conditions and organism types.
• Dynamic Noise Filtering: Applies dynamic filtering techniques to reduce noise and improve transcript accuracy.
• Merging Multiple Assemblies: Merges multiple assemblies into a coherent output using a robust algorithmic framework.

Scientific Applications:

• Non-model organism transcriptomics: Reconstructs transcripts for organisms lacking reference genome sequences.
• Benchmarking on mammalian RNA-seq: Tested on human and mouse RNA-seq data and reported improvements over transABySS and Trinity.
• Gene regulation and splicing studies: Capable of handling complex splicing events and diverse expression levels for studies of gene regulation.

Methodology:

Utilizes preliminary assemblies generated by Velvet, clusters contigs into loci, constructs transcript isoforms using paired-end and long-read information when available, and employs an array of hash lengths to optimize assembly fidelity.