TruSeq Phasing Analysis Informatics Overview

The TruSeq Phasing Analysis App consists of a suite of novel algorithms designed to provide whole-genome phasing information using the synthetic long-read sample preparation technology from Illumina. The TruSeq Phasing Analysis App uses the variants discovered from a previous deep whole-genome sequencing (WGS) run and the base calls from a long fragments library as input.

The first stage of the phasing algorithm identifies contiguous segments of haploid fragments, or clouds, in each well. In the next stage, local phasing, clouds with overlapping heterozygous SNP sites are joined, resulting in blocks that are normally around 5–10× larger in size than the input clouds. At the final stage of the analysis, global phasing, the local blocks that have been computed are phased using the 1000 Genomes phased reference panels to form long haplotype contigs.

The TruSeq Phasing Analysis App reports haplotype blocks across the genome and confidence scores for the phasing in a phased VCF file.

See TruSeq Phasing Analysis Methods for a more detailed description.

Figure 1   Overview of TruSeq Phasing Analysis Algorithm Workflow