Long read assemblers struggle to distinguish closely related strains of the same species and collapse them into a single sequence. This is very limiting when analysing a metagenome, as different strains can have important functional differences. We present the first version of a new software called HairSplitter, which recovers the strains from a strain-oblivious assembly and long reads. The originality of the method lies in a custom variant calling step that allows HairSplitter to work with erroneous reads and to separate an unknown number of haplotypes. On simulated datasets, we show that HairSplitter significantly outperforms the state of the art when dealing with metagenomes containing many strains of the same species.