A promising technology to deal with haplotype assembly in a cost-effective manner is 10x Genomics. At the beginning of 2016, the company launched their Chromium platform. The core technology is a Gel bead inside Emulsion (GEM) and uses droplet microfluidic technology prior to standard (Illumina) sequencing to generate “linked reads” that can be used to piece together haplotypes. Examples of success currently focus on the diploid human genome (www.10xgenomics.com). The existing 10x Genomics bioinformatics package for data processing contains several standard public software tools (BWA, GATK) as well as specific software tools for alignment, variant calling, de novo assembly and visualization (Long Ranger, Supernova Assembler and Loupe). Adapting these pipelines to the challenges from plant species will be a priority. Right now, the 10x Genomics software is fully focused on human samples. While haplotypes can be phased to some extent for diploid (human) data, no accepted phasing method exists yet for polyploid genomes.
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