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.

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 (CWI), The Netherlands

Baaijens, J., Stougie, L., & Schönhuth, A. (2020). Strain-aware assembly of genomes from mixed samples using flow variation graphs. In International Conference on Research in Computational Molecular Biology, RECOMB 2020 (pp. 221–222). doi:10.1007/978-3-030-45257-5_14