Hello Members,
I need your guidance in selecting k-mer for assembling bacterial genome, paired end using SPAdes.
I know and have read section
SPAdes is smart enough to select its own K-mer, and assemble thereafter.
My question is:
I'm automating assembly and downstream analysis for isolates over 1000. I'd like to understand how to select an optimal K-mer based on read length.
If I were to set K-mer based on read length, what should be those? And why?
Currently, I'm having Illumina 150X2 data.
K-mer(s) may differ based on coverage too. But lets say I've data of coverage less than 30X.
I came across below URL too.
Also, there are tools like k-mer genie and velvet_optimizer. (I've not tried them yet)
There's no recipe for these (k-mer, coverage) kind of situations, but there has to be an optimal way which might help to have reasonable output and results?
I need your guidance in selecting k-mer for assembling bacterial genome, paired end using SPAdes.
I know and have read section
SPAdes is smart enough to select its own K-mer, and assemble thereafter.
My question is:
I'm automating assembly and downstream analysis for isolates over 1000. I'd like to understand how to select an optimal K-mer based on read length.
If I were to set K-mer based on read length, what should be those? And why?
Currently, I'm having Illumina 150X2 data.
K-mer(s) may differ based on coverage too. But lets say I've data of coverage less than 30X.
I came across below URL too.
Also, there are tools like k-mer genie and velvet_optimizer. (I've not tried them yet)
There's no recipe for these (k-mer, coverage) kind of situations, but there has to be an optimal way which might help to have reasonable output and results?
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