This is the Linux app named Transcriptome assembly ORA whose latest release can be downloaded as saccharomyces_cerevisiae_3Mreads_ordered.sam.gz. It can be run online in the free hosting provider OnWorks for workstations.
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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.
This is an application that can also be fetched from https://sourceforge.net/projects/transcriptomeassemblyora/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.