abyss: troubleshoot assembly

Question

[yp19]

Hi all,

I just ran abyss on 250bp paired end reads and the assembly statistics do not look so good. Overall there are a lot of scaffolds (highly fragmented), the N50 is very low, and the total sum is way larger than what I would expect for the genome I am working on.

Here are the scaffold statistics from abyss:

n:500   n50  L50          min   max        sum
72859   802 22098         500   19251   5.93e+07

I am wondering what trouble shooting steps you would take to figure out what is causing this poor assembly. I have coverage in the range of 1000-1500X so I don't think coverage is the issue.

Thanks for all your thoughts on this.

[Brice Sarver]

Did you do the assembly across a range of k-mers and compare?

[yp19]

Above is with k-mer of 64. I also tried a k-mer of 96 but this did not improve the stats (they were more or less the same as above)

[h.mon]

Did you perform raw reads quality control and remove adapters and other contamination?

[yp19]

QC yes and removed contaminating reads, but I seem to have forgotten about adapters. I will remove them and re run. thank you for that!

[h.mon]

Please do not delete posts. The purpose of this site is two-fold: more immediately, to help people with their questions; but on the long run, to serve as a repository of knowledge. The second purpose is defeated if people delete their questions.