Workflow: Improving plant genome assemblies with Pore-CLiterature
Date: 18th March 2022
Pore-C is an end-to-end workflow combining chromatin conformation capture (3C) with long nanopore sequencing reads, providing contact information that allows existing assemblies to be scaffolded to high contiguity. Whilst traditional 3C methods typically only detect pairwise interactions between two genomic loci, Pore-C generates higher-order contact information from multiple genomic loci. The method is amplification-free, enabling access to GC-rich and repetitive genomic regions. Epigenetic modifications are also preserved in the long nanopore reads and can be characterised alongside nucleotide sequence. Together with high-output PromethION™ Flow Cells, highly contiguous, chromosome-scale plant genome assemblies are now possible.
Here we present a complete workflow for the scaffolding of a plant genome assembly to the chromosome scale.