Question: k mer analysis
0
gravatar for Mostafa
21 months ago by
Mostafa20
Mostafa20 wrote:

Hi everyone!

I am wondering to do a k mer analysis on my input 10X reads lib which has been pre processed by longranger basic. It aims to find the best k value for my assembly.

I thought that KAT can help me. but it seems that it does not apply the different k values

does anyone know the proper tools or R package?

kmer analysis assembly k-mer • 687 views
ADD COMMENTlink written 21 months ago by Mostafa20

If your aim is to do de novo assmebly then definitely look at Supernova which is 10x's assembler. It can make use of 10x specific features in your data.

Jellyfish is a popular k-mer analysis tool.

ADD REPLYlink modified 21 months ago • written 21 months ago by genomax90k

Thanks. Actually, we have not observed expected results on from Supernova and are exploring for the reasons in analytical step.

ADD REPLYlink written 21 months ago by Mostafa20

Did you have an adequate amount of data? Supernova requires at least 30x coverage, but more is better.

ADD REPLYlink written 21 months ago by genomax90k

our coverage is almost good, but the genome is highly repetitive and we are aware that more coverage could be helpful. However, the result is much weaker than you would think about the coverage.

ADD REPLYlink written 21 months ago by Mostafa20
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