Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, Jain M, Paten B.

Nat Biotechnol. 2020 Sep;38(9):1044-1053. doi:10.1038/s41587-020-0503-6

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.

Runs in memory (no disk IO) and requires terabyte amounts for human genome. Designed for Nanopore data. Reads are run length encoded before assembling. Assemblies are more fragmented, but with less disagreements to the reference. The estimated cost of running is lower than for competitors.