The news broke on Twitter; I missed in the first time but then it popped in my feed some days later
The discontinuation is presumably a side effect of 10X's recurring defeats in patent battles with BioRad over the technology used in their early products. When deciding what to reformulate into their newer formats that 10X believes are clear of BioRad's intellectual property, they have apparently decided to not go forward with the genome sequencing kits.@10XGenomics is abandoning their genome assays - likely due to IP issues. This is a shame since the enabled fantastic genome assemblies for mammals, birds, and reptiles from HQ DNA.— Lutz Froenicke (@DNATech_Lutz) January 10, 2020
They have NOT announced yet if they will re-brand their company as 10XTRANSCRIPTOMICS. ;-) pic.twitter.com/PX3Y5GwU57
I had sometimes kept tabs on de novo assemblies of large genomes made with 10X libraries. While it was challenging to find ideal pairs of projects for comparison, the general impression I had is that 10X could do a good job, but the scaffold N50 for a 10X-boosted genome assembly would typically be in the range of the contig N50 for a true long read (PacBio or Oxford Nanopore) genome. So all other things being the same, you'd have higher overall contiguity using true long reads.
Of course, cost, workflow and input material can be very important considerations. With Sequel II on the PacBio side and PromethION for Oxford, the cost advantage of linked reads on Illumina has been shrinking. For workflow, the overall workflow on the library prep is probably not radically different, though not being in the lab I'm not the best source on this. 10X did require only 10 nanograms of input, but now PacBio has an ultra low input prep down in that size range. Both of those companies have de novo genomes and haplotyping as primary foci; these platforms are boosting performance at a rapid clip.
Perhaps also influencing 10X's decision is the launch of TELL-Seq from Universal Sequencing Technology. This is a kit that claims to generate linked reads from DNA samples using bead-bound transposases, but without any droplets or specialized hardware. If this really works nearly as well as 10X on functional criteria, then TELL-Seq would be very difficult to compete with on cost and workflow: it's a very simple Nextera-style workflow potentially amenable to automation and with no capital costs.
There are companies with similar products in the wings for single cell transcriptomics, so perhaps 10X decided to sacrifice a niche product with limited growth potential in favor of focusing on their core. They also want to be the dominant player in spatial transcriptomics, and there are lots of potential competitors there. So an apparent choice to focus at the expense of their oldest product line.