Question: assemblers choose high k-mers: what does that mean?
0
gravatar for willnotburn
2.3 years ago by
willnotburn40
United States, Michigan State Universtiy
willnotburn40 wrote:

I am co-assembling metagenomic PE reads. megahitand metaSPAdesconsistently choose the final assembly as one based on the longest k-mer (141).

What does that tell about my input data and the assembly? Any cause for joy or concern?

metagenomic assembly • 1.6k views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by willnotburn40
3
gravatar for genomax
2.3 years ago by
genomax91k
United States
genomax91k wrote:
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by genomax91k

Thanks, genomax. A lot in 1st and 3rd papers is - and will likely always be - outside of my field.

But I am happy to have gleaned one thing from your second bullet point. If the best k-mer length is often 80% of read length, then the longest available k-mer (141 for megahit and 127 for metaSPAdes) would make sense for my input data, which is PE 250bp.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by willnotburn40
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