Hello all, 

I was wondering if there is a guide to modern genome assembly - that is, what often involves both short and long reads, as well as Hi-C sometimes? 
What tricks can be used for typical problems (contaminated reads, highly heterozygous genome, etc)?

Thank you in advance, as always
There are some guidelines from the Earth BioGenome Project here: https://www.earthbiogenome.org/assembly-standards

These address quality requirements and standards rather than how to achieve them, but they also mention the  [Vertebrate Genome Project assembly pipeline][1]. It might be useful to look at the tools VGP pipeline use and related publications, e.g. the [Rhie et al., 2021 paper][2]. Indeed, the Methods and Supplementary might sufficiently address the issues you mention. 

What helps against highly heterozygous genome, btw? High levels of inbreeding over many, many generations (but that has maybe fallen out of fashion).


  [1]: https://github.com/VGP/vgp-assembly
  [2]: https://www.nature.com/articles/s41586-021-03451-0