Decipher RNA isoform combinations from minigene splicing assays and massive parallel sequencing with MAGIC

Summary Functional testing of RNA using minigene splicing assays is increasingly being realised to demonstrate the effects of variants on splicing. In complex cases, variant pathogenicity is assessed by Sanger sequencing, which can be time consuming and may be replaced by short read sequencing. Moreover, strategies based on long read sequencing of the amplified minigene construct are promising and allow the isoforms to be fully characterised. We introduce MAGIC, a user-friendly tool that first generates the artificial construction genome files required to then perform alignment, assembly and annotation of the isoforms obtained by either short or long read minigene splicing assay sequencing. Availability and Implementation MAGIC is available at https://github.com/LBGC-CFB/MAGIC. Zenodo DOI: 10.5281/zenodo.17052752. Supplementary information Supplementary data are available at Bioinformatics online.