Coverage for de novo genome and transcriptome assembly of unknown size

Question

[kris_A]

Hello everyone,

I was asked this one question I don't really know the answer to and was hoping someone could help. A group is sequencing genome and transcriptome of unknown sizes and is wondering what should the coverage be to ensure successful assembly using HiSeq (250bp read length). Maybe someone can link me to some good material or give some indications on how to make this decision. Thank you for your time and help in advance.

Best, Kristina

Answer 1

[Medhat]

which species? what is the complexity of the genome?
A field guide to whole-genome sequencing, assembly and annotation

Sequencing depth and coverage: key considerations in genomic analyses

general answer would be 50 and 100x

[kris_A]

it's a fly species with a potentially high complexity. But thanks for the resources, will read through.