SAMI

SAMI detects aberrant splicing events in short-read RNA-seq data, focusing on identifying non-recurring events in low-dimension data.

Key Features:

• UMI-aware analysis: SAMI incorporates Unique Molecular Indexes to improve detection accuracy of splicing events.
• Annotation-differential splicing detection: SAMI focuses on splicing events which differ from provided annotation.
• Intrageneic splicing aberration detection: SAMI detects splicing abnormalities occurring within single genes.
• Gene fusion detection: SAMI identifies fusion events between different genes.

Scientific Applications:

• Routine diagnostics: SAMI addresses identification of non-recurring splicing events in low-dimension data common in clinical diagnostic settings.
• Benchmarking and validation: SAMI performance was assessed on real data from a commercial control sample and simulated data generated with ASimulatoR.

Methodology:

SAMI is implemented as a Nextflow pipeline and Singularity container.