Table 2.
Comparison with the different pipelining systems available
| Function | TOGGLE | GATK-Queue | HugeSeq | Churchill | GotCloud | bcbio-nextgen |
|---|---|---|---|---|---|---|
| Raw FASTQ Data | Y | N | N | N | N | Ya |
| Reference indexing | Y | N | N | N | N | Ya |
| FASTQ to final Data | Y | N | Y | Y | Y | Y |
| Multiple Samples Calling | Y | Y | Y | Y | Y | Y |
| Modularity | Y | Y | N | N | Y | Y |
| Between Sample Paralellization | Y | Y | Y | Y | Y | Y |
| Within Sample Parallelization | Y/Nb | Yb | Y | Y | Y | Y |
| Structural Variant Analysis | N | N | N | Y | Y | N |
| Annotation | Ya | Y | N | Y | Y | Y |
| Scalability | Y | Y | N | Y | Y | Y |
| Evolutivity | Y | Y | Y | Y | Y | Y |
Y signals that a feature is present, N is absent. Evolutivity means the possibility to add future module or functions to the system
aAvailable as separated steps
bDepending the considered step