Assembly tool comparison

[Mehmet Göktay]

Hi everyone,
I'm planning to assembly a plant genome. The data comes from miSeq 2x300 paired-end and the output size about 15Gb.

Our aim is not get complete assembly, we are just planning to find ssrs on the contigs nothing else.

My question is, do you think that I can reach my aim? If so, which assembly tool you would suggest? (Abyss, mira etc.)

[westerman]

It depends on the plant's genome size. They do vary a lot! Don't use Mira, while nice it will bog down. ABySS is generally good.

[Mehmet Göktay]

I suppose genome size will be about 900 Mb. So approximately coverage will be about 10x.

[westerman]

It will be tough to assemble at 10x but you will get some data. I am currently finishing up an SSR project on a plant of around 1100 MBases. We had around 15x coverage and were able to detect SSRs. Useful ones, we hope, but further lab work will be needed to verify.

[Mehmet Göktay]

Which NGS platform did you use? İllumina miSeq,454 or anything else?
And if I'm not asking too much? Which assembly tool did you use for this data?

[westerman]

hiseq2500.

I used ABySS followed by QDD for SSR calling.

[Mehmet Göktay]

Thank you for your kind answers. They are very helpful to me.