05 Jun 2020
There’s not much to say about Purge Haplotigs that isn’t already covered in the paper and documentation. Instead I’ll talk about my impressions and experience with creating a bioinformatics software package.
26 May 2020
Continuing from Chardonnay Part 1: The Reference Genome, the second part of this project involved the identification of SNP and InDel markers that can distinguish the different clones of Chardonnay. The biggest challenge for this aspect was filtering out the hundreds of thousands of false-positive markers, from the millions of heterozygous variants, to identify the few thousand true marker SNPs and InDels.
19 May 2020
Chardonnay was the second grapevine genome to be assembled using third-generation long read sequencing. Like the Cabernet Sauvignon genome, FALCON-Unzip was used to generate a ‘diploid’ assembly. The assembler, sequencing technology, and the concept of diploid assemblies were relatively new at the time so there were several hurdles to overcome before the Chardonnay reference genome was ready for our clonal marker work. Continued in Chardonnay Part 2: Clonal Marker Discovery