Hi there,
I have recently assembled a NGS HiSeq data with ABySS 2.02. With the default setting (K-mers=64) I had a 183nt stretch of N (or Gap). I have changed k-mer to 40 and the gap reduced to 165nts. Furthermore, k-mers=20 has also performed and I have observed NO Gap containing N sequences. I want to ask you what exactly can I conclude from this result. More importantly, I want to know if my last result, which has no N sequence, is reliable to further analysis.
Regards
Alireza
The short answer is "no". The proper selection of k-mer size influences the correct assembly of contigs. Which afterwards, can be verified.
Here is a recent paper that includes references to programs designed to optimize the correct k-mer size for assembly and proposes an alternative empirical method to determine the proper k-mer size to use..
Optimizing k-mer size using a variant grid search to enhance de novo genome assembly. Soyeon Cha and David McK Bird. Bioinformation. 2016; 12(2): 36–40.
Published online 2016 Apr 10. doi: 10.6026/97320630012036
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5237644/
Dear James
May I aks you how to interpret ABySS statistical results?
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