Assembly size is double the genome size despite specifying --genome-size in flye

Question

[gilmahu]

Dear All,

I have used flye to assemble two nanopore reads. One looks fine but one assembly even after the polishing step is twice the size of the genome size (i.e. 9.5MB instead of a maximum of 5MB). And this happened despite that I specified a --genome-size of 5m. Here is the command within my script: for f in *.fastq; do flye --nano-corr {$f%}_outflye; done.

Does anyone have an idea what could have gone wrong and how to fix it?

PS: The filtered size of the two reads were around 900MB... i just can't figure out why one is misbehaving

Looking forward to any help out there.

Best regards

[5heikki]

Contamination?

[samuel.a.odonnell]

I don't think you'll find any specific answers here except to have a look at what was assembled and see if it is all from your species of interest, if it could be highly heterozygous or a hybrid etc

You could quickly align your two assemblies and generate a dotplot as a first step.

Answer 1

[gilmahu]

Thank you guys for the comments. I think contamination could be the issue. I will check this with kraken and find a way out. Thanks a lot.