KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 1G reads. Its memory consumption is around 5Gb for 100M reads. KisSplice is not a full-length transcriptome assembler. This means that it will output the variable regions of the transcripts, not reconstruct them entirely.
module spider kissplice to find out what environment modules are available for this application.
- HPC_KISSPLICE_DIR - installation directory
If you publish research that uses kissplice you have to cite it as follows:
Gustavo AT Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo* and Vincent Lacroix*, KISSPLICE: de-novo calling alternative splicing events from RNA-seq data, BMC Bioinformatics 2012, 13(Suppl 6):S5