Hi-C sequencing and costs

[ps]

Hi Olga and all,

I'm just starting out with genomics for a PhD project so excuse me if the questions are too basic. I need to assemble the genome for my study species (a small squirrel) before i can do other analyses so I'd like to do that using Hi-C and I'm excited about the prospect of the $1000 genome assembly. My basic questions are

1. In terms of sequencing, I would need to do only short read sequencing (illumina) and Hi-C sequencing before I start thegenome assembly with Juicebox, is that correct? Any other sequencing work (or lab work, assuming the sequencing labs will take care of library building) that I might need to outsource just to make sure that I have everything ready before I start assembly on a computer?

2. I've asked just a couple labs and Hi-C sequencing costs are closer to $9000 than $1000. Do you guys have any recommendation for getting this done at a cheaper rate? Labs in the UK would be preferred but anywhere else would work too. 

Thanks everyone!

PS

[Olga Dudchenko]

Hi PS,

1. When you say sequencing that should imply library preparation and sequencing.

2. I assume the labs/companies have given you quotes for long-read-based sequencing and assembly.

Best,

Olga