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abyss: troubleshoot assembly

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.

abyss assembly
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written by yp19 yp19

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

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written by Brice Sarver Brice Sarver

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)

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written by yp19 yp19

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

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written by h.mon h.mon

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!

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written by yp19 yp19

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.

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written by h.mon h.mon

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