Any comparable alternatives to linked read sequencing?
I read that 10X Genomics discontinued its linked-reads technologies:
Discontinuation of Linked-Reads At 10x Genomics, we are committed to enabling your research and providing you with >the best experience to make scientific discoveries. Earlier this year, as a part of >our product life cycle management, we notified you about refinements to some of our >on-market product offerings.
As of June 30, 2020, we discontinued the sale of our Chromium Genome and Exome >product lines. We will not be releasing new versions of these products.
We thank you for your partnership and are committed to providing the highest-quality >technical and software support.
Please contact your Sales Executive, Field Application Scientist, or email our >Support Team at email@example.com with any questions.
See here on the 10X Genomics homepage.
This source assumes the product was discontinued due to...
infringed patents held by Bio-Rad Laboratories...
But when searching for "linked-reads" and "Bio-Rad" I cannot find anything. Having worked with ddPCR I assume 10X Genomics problem was the oil emulsion but not the linked-reads approach?
Is there an alternative platform doing what 10X Genomics linked-reads was able to accomplish? I am specifically interested in its role in genome assembly/scaffolding as in the Vertebrate Genome Project (in bold):
The current pipeline (Figure 1) to meet the 3.4.2.QV40 phased metric with the fewest errors currently achievable consists of a combination of the following approaches:
- 60X PacBio long-reads for an initial phased contig assembly (30X/haplotype);
2. 68X coverage of 10X Genomics-linked reads for intermediate-range scaffolding and further phasing (34X/haplotype);
- 80X Bionano optical maps to correct scaffolding errors and for further scaffolding;
- 68X Hi-C linked reads for long-range scaffolding; PacBio Jelly algorithm to fill gaps using long-reads;
- 10X Genomics Illumina short-reads for base-call accuracy polishing; and
Thanks for your insights!