The goal of strain-aware genome assembly is to reconstruct all individual haplotypes from a mixed sample at the strain level and to provide abundance estimates for the strains.

dx.doi.org/10.1007/978-3-030-45257-5_14
Lecture Notes in Computer Science/Lecture Notes in Artificial Intelligence
International Conference on Research in Computational Molecular Biology
Centrum Wiskunde & Informatica, Amsterdam, The Netherlands

Baaijens, J.A, Stougie, L, & Schönhuth, A. (2020). Strain-aware assembly of genomes from mixed samples using flow variation graphs. In Lecture Notes in Computer Science/Lecture Notes in Artificial Intelligence. doi:10.1007/978-3-030-45257-5_14