Question: How to extract reads that match k-mer profiles from a collection of sequences?
gravatar for O.rka
9 weeks ago by
O.rka70 wrote:

Let's say you had 10 draft-genome assemblies from different sources with 100 contigs all together from a particular genus.

Are there any tools that allow you to use this "database" of assemblies to then grab any reads that have even a remotely similar k-mer usage to the "database"?

I know about kneaddata but that is mapping to a very specific reference sequence, I'm looking for a way to extract reads that have similar k-mer usage.

Is there a tool that I can use to do this?

sequencing • 197 views
ADD COMMENTlink modified 9 weeks ago by genomax59k • written 9 weeks ago by O.rka70

You can use mash ( ), sourmash ( ) or from BBMap suite ( ) can help you with the classification but I am not sure if they have functionality to extract those reads.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by genomax59k ?

ADD REPLYlink written 9 weeks ago by shenwei3564.3k
gravatar for genomax
9 weeks ago by
United States
genomax59k wrote:

cookiecutter ( ) seems to do what you need. You will need to test and ascertain.

ADD COMMENTlink written 9 weeks ago by genomax59k

Is that more for extract adapters or can it be extended to entire genome k-mer profiles?

ADD REPLYlink written 8 weeks ago by O.rka70
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