Question: k mer analysis
gravatar for Mostafa
9 weeks ago by
Mostafa10 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 • 167 views
ADD COMMENTlink written 9 weeks ago by Mostafa10

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 9 weeks ago • written 9 weeks ago by genomax62k

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

ADD REPLYlink written 8 weeks ago by Mostafa10

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

ADD REPLYlink written 8 weeks ago by genomax62k

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 8 weeks ago by Mostafa10
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