Question: PacBio genome assembly with canu shorter than expected
1
gravatar for Rob
6 weeks ago by
Rob70
Rob70 wrote:

Hi,

I have ~70x PacBio reads and I did an assembly with Canu. I expected a 216 Mb genome but I got a 146Mb assembly of 465 contigs with 1.3G of unassembled data.

I tried to modify some parameters, for overlap length or coverage, but I can't get an assembly which reach the size I wanted (it just increase the number of contigs, or did nothing visible).

Is there any way to improve the size of my assembly by adjusting assembler's parameters, or maybe is there a possible problem with my data? (I didn't polish my data yet, because I have trouble with quiver atm, but I don't expect quiver to up the size of my assembly, am I right?)

What can explain this difference? And what can I do for that?

Thanks for your help!

canu pacbio assembly genome • 210 views
ADD COMMENTlink written 6 weeks ago by Rob70
1

Did you try first to correct your read using any self correction method like https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/ then assemble and see the results?

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Medhat6.1k

I assume Canu correct the reads by itself, so no, I didn't correct them. But I will try your tool, it seems useful.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Rob70
1

you are right

Canu will correct the reads

I missed it

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Medhat6.1k
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