Table 1. Software packages used to identify and quantify structural variation.
| Abbreviation | Breakpoint Identification | Alignment | Assembly |
|---|---|---|---|
| gsnap/Cufflinks | gsnap | tophat | Cufflinks |
| gsnap/StringTie | gsnap | tophat | StringTie |
| STAR/Cufflinks | STAR | STAR | Cufflinks |
| STAR/StringTie | STAR | STAR | StringTie |
| HISAT/Cufflinks | HISAT2 | HISAT2 | Cufflinks |
| HISAT/Stringtie | HISAT2 | HISAT2 | Stringtie |
An abbreviation is indicated for each of the six structural variant assemblies generated, as well as the software packages used for each step.