Note: This was originally conceived as a companion to the paper “Human Genome Assembly in 100 Minutes.” At the time in 2019, some of these points were controversial, but now they seem almost passe. Indexing-based approach to assembly reduces the algorithmic complexity from a quadratic scalability, where every read is compared to every read, to a situation in which each read is represented indexed locations of ‘minimizer k-mers’. A very good assembly can be constructed simply by computation on the indicies rather than the reads themselves.

Human Genome Reference Remains Incomplete When I was still a physics graduate student, I heard about the coolest thing at the time: we finished the Human Genome Project. It made me think about how awesome we can get all those little letters A/C/G and T in each of our cells. There must be a lot of human health and medicine problem that we can solve with the new information about our genomes.