Nicolas Dierckxsens

gzip should work, maybe something went wrong with the compression of the file. So you could try to unzip and then gzip it again... Or maybe you have a very...

I can't see the files, think you should send to my private email or on the github chat itself

Hi it works fine for me, so I am not sure what the problem is. I had one user who had a similar problem, he found the problem himself, this...

ok great! maybe will have a look if I can prevent that it causes a problem

@dinhe878 Are those illumina reads? How can you link the paired reads, because only one of the 3 pairs having matching IDs? And can you send me the log too?

Those reads could still bu run as SE reads but not as PE

I could be a repetitive control region, which are very hard to assemble with short reads. Have you checked if the second contig is repetitive?

For repetitive control regions, it's no point in giving a reference, there is to much variation, even between individuals of the same species. Run it again without the reference with...

Hi, Depends on the size of your accepted genome. For chloroplast genomes I used to take 120000-200000

It will try to circularize the assembly within this range by looking for overlaps on both ends of the assembly