Resulting contig is way longer than expected

[kaanb93]

Hello,

First of all, thank you very much for such an amazing tool, I've been using it for a while.

On my last assembly, I'm trying to assemble a viral genome with Illumina Novaseq 2x150 reads. Even though I have tried --gsize 10k, I'm ending with only a single contig which is 100k long.

Full code:

shovill --keepfiles --outdir assembly --mincov 2 --minlen 200 --gsize 10k --R1 raw_data/AP_T65_1.fq.gz --R2 raw_data/AP_T65_2.fq.gz

Why does this happen? Is there anything that I could do to limit contig length somehow?

Sincerely,

Kaan

[wvnicholson]

I'm interested in the answer to this question as well and I have a related question which I may post later. It doesn't look there have been any responses to issues for about three years though? Also, no new code for four years,

William