devider: long-read reconstruction of many diverse haplotypes

Reconstructing haplotypes is important when sequencing a mixture of similar sequences. Long-read sequencing can connect distant alleles to disentangle similar haplotypes, but handling se-quencing errors requires specialized techniques. We present devider, an algorithm for haplotyping small sequences--such as viruses or genes--from long-read sequencing. devider uses a positional de Bruijn graph with sequence-to-graph alignment on an alphabet of informative alleles to provide a fast assembly-inspired approach compatible with various long-read sequencing technologies. On a synthetic Nanopore dataset containing seven HIV strains, devider recovered 97% of the haplotype content compared to 86% for the next best method while taking 8000x coverage. Benchmarking on synthetic mixtures of antimicrobial resistance (AMR) genes showed that devider recovered 83% of haplotypes, 23 percentage points higher than the next best method. On real PacBio and Nanopore datasets, devider recapitulates previously known results in seconds, disentan-gling a bacterial community with > 10 strains and an HIV-1 co-infection dataset. We used devider to investigate the within-host diversity of a long-read bovine gut metagenome enriched for AMR genes, discovering 13 distinct haplotypes for a tet(Q) tetracycline resistance gene with > 18, 000x coverage and 6 haplotypes for a CfxA2 beta-lactamase gene. We found clear recombination blocks for these AMR gene haplotypes, showcasing deviders ability to unveil ecological signals for heterogeneous mixtures.