Detection of various kinds of polymorphisms in RNA-seq data

 KisSplice is a piece of software that enables the analysis of RNA-seq data
 with or without a reference genome. It is an exact local transcriptome
 assembler that allows one 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.