Method | Extensive documentation | Standard file formats | Gene-level estimates | Reconstruction supported | DE analysis | Efficient multi-threading | Fast | Small memory footprint |
---|---|---|---|---|---|---|---|---|
BitSeq | X | X | Â | Â | X | X | Â | Â |
CEM | Â | X | Â | X | Â | Â | X | X |
Cufflinks | X | X | X | X | X | X | Â | Â |
eXpress | X | X | Â | Â | X | Â | Â | X |
IsoEM | Â | X | X | Â | Â | X | X | Â |
MMSEQ | X | X | X | Â | X | Â | Â | X |
RSEM | X | Â | X | Â | X | X | Â | Â |
rSeq | X | Â | X | Â | Â | Â | Â | X |
Sailfish | X | X | Â | Â | X | X | X | X |
Scripture | (X)* | X | Â | X | Â | Â | Â | Â |
TIGAR2 | X | X | Â | Â | Â | Â | Â | Â |