3D-DNA pipeline parameters of Plant genome in the DNAzoo website

[Zhigui Bao]

Hi, Olga

3D-DNA pipeline is very powerful for the genome scaffolding, especially when I saw the Petunia axillaris genome. 

The draft assembly looks are very fragment and the chromosome-length have a amazing contact maps. But how the parameter tuning process going? Does it run in the default paraments of 3D-DNA? Given that plant genome always have more repeat elements and more chance to assembly a high heterozygous genome. Would you provide the detailed command for the DNAzoo plant genome.

Bests, 

Zhigui Bao

[Olga Dudchenko]

Hello Zhigui,

There isn't anything specific to plants that I could recommend tuning. Most of variability comes form drafts and the error modalities that creep up, and those are very different depending on seq techonologies, contiggers/prescaffolders and their combinations. Some of the typical scenarios are briefly named in cookbook: undercollapsed heterozygosity, coverage biases, alignability issues, gaps in draft sequences etc. The good news here is that the pipeline outputs all the necessary information to help recognize the typical error modality, see if defaults are handling it well and tune if not. Run the defaults to .0. step and first editing, load the map, load the relevant .bed and .wig tracks, and take it from there, would be my recommendation...

Thanks for the kind words and hope this is of some help,

Olga