intronSeeker identifies potentially retained introns in de novo RNA-seq assembly in order to quantify and remove them. To use it you have to provide a set of contigs resulting of a de novo transcriptome assembly and a set of RNA-Seq reads. The reads will be aligned on the contigs, splices sites will be searched and tested to check if they correspond to valid intron retention events. The tool works by aligning user-provided reads to contigs from a de novo transcriptome assembly. Splice sites are then searched and tested to check if they correspond to valid intron retention events. intronSeeker provides a list of potential intron candidates, it filters them and outputs a clean reference without introns in Fasta format