What SALMON method does FLAIR quantify use when called with --salmon?

[bayraktar1]

Hi,

When running FLAIR quantify you can specify --salmon to have the quantification done by SALMON.

The SALMON documentation mentions that there is a mapping-based and alignment-based method. What SALMON quantification method does FLAIR call when the --salmon flag is used?

I was not able to find an answer on the wiki.

Thanks,

[bayraktar1]

From the published FLAIR paper: """We evaluated salmon as a quantification tool using its alignment-based mode with all minimap2 alignments, as performance of the quasi-alignment mode could suffer from low read accuracy."""