After running the pipeline on my own data (paired PacBio HiFi and Arima high-coverage Hi-C for the same individual), I found that manually curating the assemblies with PretextView would not be possible because the pretext files appear to lack contact information. I'm including a screenshot of the directory contents for the Hi-C contact maps as well as the PretextSnapshot output from the pipeline and a Juicer visualization of the .hic file. This was run using Nextflow version 26.04.1.12112 and sanger-tol/genomeassembly 1.0.0dev
The PretextSnapshot for this haplotype assembly:
And a screenshot taken from visualizing the .hic output in Juicer:
I am happy to share the config files I used to run the pipeline, but it seems like I can only attach images?
After running the pipeline on my own data (paired PacBio HiFi and Arima high-coverage Hi-C for the same individual), I found that manually curating the assemblies with PretextView would not be possible because the pretext files appear to lack contact information. I'm including a screenshot of the directory contents for the Hi-C contact maps as well as the PretextSnapshot output from the pipeline and a Juicer visualization of the .hic file. This was run using Nextflow version 26.04.1.12112 and sanger-tol/genomeassembly 1.0.0dev
The PretextSnapshot for this haplotype assembly:
And a screenshot taken from visualizing the .hic output in Juicer:
I am happy to share the config files I used to run the pipeline, but it seems like I can only attach images?