Supporting data for "HaploMaker: An improved algorithm for rapid haplotype assembly of genomic sequences"

In diploid organisms, whole genome haplotype assembly relies on the accurate identification and assignment of heterozygous single nucleotide polymorphism (SNP) alleles to the correct homologous chromosomes. This appropriate phasing of the alleles ensures combinations of SNPs on any chromosome, called haplotypes, can then be used in down-stream genetic analyses approaches including determining their potential association with important phenotypic traits. A number of statistical algorithms and complementary computational software tools have been developed for whole genome haplotype construction from genomic sequence data. However, many algorithms lack the ability to phase long haplotype blocks and simultaneously achieve a competitive accuracy. <br>In this research we present HaploMakerr, a novel reference-based haplotype assembly algorithm capable of accurately and efficiently phasing long haplotypes using paired-end short reads and longer PacBio reads from diploid genomic sequences. To achieve this we frame the problem as a directed acyclic graph with edges weighted on read evidence and use efficient path traversal and minimization techniques to optimally phase haplotypes. We compared the HaploMaker algorithm with three other common reference-based haplotype assembly tools using public haplotype data of human individuals from the Platinum Genome project. With short read sequences, the HaploMaker algorithm maintained a competitively low switch error rate across all haplotype lengths and was found to be superior in phasing longer genomic regions. For longer PacBio reads, HaploMaker remained competitive for small block lengths and managed to generate longer block lengths than the competing algorithms. <br>HaploMaker provides an improved haplotype assembly algorithm for diploid genomic sequences by accurately phasing longer haplotypes. The computationally efficient and portable nature of the Java implementation of the algorithm will ensure it has maximal impact in reference-sequence based haplotype assembly applications