Transcriptome assembly ORA

Sofware for reference-based transcriptome reconstruction. It performs reconstruction starting from short reads obtained from RNA-seq. It is best suited to manage the transcriptomes of lower eukaryotes with a low number of introns per gene and it can be used also for procariotes.
It needs a SAM file with the reads aligned on the reference genome and (optional) a gff file with the position of genes on the reference genome.
It provides in output the positions of the transcripts identified, the transcripts names based on the genes present on the gff file anf the size of UTR regions.