Anti-retroviral therapy (ART) is used to treat HIV infections by inhibiting viral replication. However, a latent viral reservoir persist despite treatment. Possible explanations for this viral reservoir persistence include clonal expansion of latently infected cells and perhaps residual viral replication. To study this, we will investigate the HIV haplotypes in individuals on long-term ART. We will develop and benchmark a bioinformatic pipeline to reconstruct HIV haplotypes from next-generation sequencing (NGS) data.