NGS workflows

Question

[Jamand]

Hello,
I'm trying to assembly a genome and I'd like to know if the following workflows are correct:
1) fastqc - velveth - velvetg - mauve ordering with a reference genome - mauve metrics
2) fastqc - velveth - velvetg - reapr to assess quality and close gap - mauve ordering with a reference genome - mauve

metrics
3) fastqc - abyss - mummer -reapr.

Can you give me any suggestion about the above workflows?
Do you know any other efficent workflow to assembly and evalute a bacterial genome?

Thanks in advance

Answer 1

[midox]

Hello,

You can use Newbler 2.8 or Platanus Assembly. They are efficient for Bacterial Genomes.