Table 6. Comparison of key features of the ISMU pipeline with similar pipelines.
| Features | ISMU | SIMPLEX | ngs– backbone | GATK | inGAP | SeqGene | GAMES | TREAT | Atlas2 |
| Free of charge | Y | Y | Y | Y | Y | Y | Y | Y | Y |
| SE/PE data handling | Y/Y | Y/Y | Y/N | Y/Y | Y/Y | n.m | Y/Y | Y/Y | Y/Y |
| NS/CS data handling | Y/N | Y/Y | Y/Y | Y/Y | Y/N | n.m | Y/Y | Y/N | Y/Y |
| Alignment | Y | Y | Y | N | Y | Y | N | Y | N |
| No. of alignment tools | 5 | 1 | 1 | N | 2 | n.m | N | 2 | N |
| Variant annotation | Y | Y | N | Y | N | Y | Y | Y | N |
| Highly customizable | Y | Y | Y | Y | N | Y | Y | Y | N |
| Homo−/heterozygosity | Y/Y | Y/Y | N/N | Y/Y | N/N | Y/Y | N/N | Y/Y | Y/Y |
| Quality reports | Y | Y | Y | Y | N | Y | N | Y | N |
| Graphical user interface | Y | N | N | N | Y | N | N | N | Y |
| Standalone | Y | Y | Y | Y | Y | Y | Y | Y | Y |
| HPC support | Y | Y | Y | Y | N | N | N | Y | N |
| Multi user support | Y | Y | N | N | N | N | N | N | N |
| Cloud support | N | Y | N | N | N | N | N | Y | Y |
ISMU is one of the few tools that provide an easy to use graphical interface (GUI) packed with a wide choice of open source tools (alignment and variant calling) for handling NGS data. The information describing features of other pipelines is derived from Fisher et al. [60] and compared. The symbols “Y” and “N” represent, presence and absence of the feature in the pipeline. Numbers (1. 5, 2) indicate number of tool included in the pipeline. “n.m” refers to feature not mentioned.