KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler, which enables 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. It is not a full-length transcriptome assembler. This means that it will output the variable regions of the transcripts, not reconstruct them entirely. However, KisSplice results can be further aligned to a reference transcriptome (if available), or to the output of a full-length transcriptome assembler like Trinity or Oases.
Contact: Vincent Lacroix