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. 2017 Mar 17;7(5):1487–1497. doi: 10.1534/g3.117.040634

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.