Genome assembly workflows for NGS

[elisacarli]

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

[GenoMax]

One thing missing is a trimming/scan step (after FastQC). If your reads are clean then this won't make any difference but if they have adapter contamination etc you would want to remove that prior to assembly.

For bacterial genomes SPAdes should also be considered as an option to Velvet. Same group makes QUAST available for evaluating genome assemblies.

[SylvainL]

Hi, which kind of data do you have? Paired-end (I hope so) or single-end? Which length?

For bacterial genome, you can also give a try to edena