Portello: Making global assembly more effective for rare-disease whole genome sequencing

Motivation Long-read de novo assembly methods provide great potential to improve whole genome sequencing analysis for rare-disease, however these methods are typically under-utilized. Among the complications of an assembly-based approach is the difficulty of reviewing read evidence for assembly-based inferences, including access to read-based information on basecall qualities, methylation, and mosaic variants not captured in the assembly consensus. An additional complication is resolving conflicts in variant representation between assembly-based inferences and those based on conventional reference-based read-mapping pipelines. Here we propose a new assembly-based mapping approach, portello, which addresses both of these issues by transferring read mappings from the sample's de novo assembly contigs onto a standard reference sequence. Results: Portello's assembly-based mapping approach results in read-to-reference alignments that can be used by standard mapping-based variant callers without modification, resulting in improved accuracy due to higher-quality mapping. This approach also enables assembly and reference mapping-based inferences to be unified onto a consistent view of the sample, and enables direct review of read-level support for the assembly consensus in the context of a standard reference genome. To demonstrate portello's impact on variant calling, we show that DeepVariant calls from portello alignments remove 47% of small variant basecall errors found in calls made from conventional read mapping. We additionally demonstrate how portello alignments can improve visualization and interpretation of complex loci, including an example where a copy number gain in a segmental duplication region can be easily inferred from assembly-based mapping while interpretation of the same region from conventional read mapping remains impractical. Portello is also capable of directly phasing and haplotagging read alignments as part of the alignment transfer process, including for partially-phased assembly contig inputs where phasing blocks need to be delineated within each contig. Availability The portello source and pre-compiled binary is released on GitHub: https://github.com/PacificBiosciences/portello.