Where it has been used
Ligase v0.1.0 was published on 20 October 2026. It has no outside users. There are no case studies here in the usual sense — nobody outside the project has reported their experience of it, because nobody outside the project has used it.
What there is, is work that has actually been run. Two pieces:
The reference pipeline, validated against published results
HIV-1 reads to drug-resistance calls, checked against the Stanford HIVdb results published by the HIVGenoPipe study. This is the project’s own work, and it is the acceptance test for v0.1’s last milestone rather than an independent assessment.
It is worth reading anyway, for two reasons. The agreement is exact at the thresholds that matter clinically, and every remaining discrepancy has a recorded cause — including one that is a genuine sensitivity limit and is described as one. And validating the pipeline is what found its largest bug, which is a more useful thing to know about a tool than its success rate.
An evaluation by a sibling project
SAWA is evaluating Ligase for HIV drug-resistance surveillance. It is a sibling project rather than a third party, and the evaluation is not a decision to adopt.
It has already found a real problem — a coordinate-system hazard in HIV pol numbering that Ligase handles silently and wrongly — which is documented on that page because a limitation found by someone trying to use the thing is worth more than a feature list.