Question: How to extract reads that match k-mer profiles from a collection of sequences?
0
gravatar for O.rka
4 months ago by
O.rka70
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 • 238 views
ADD COMMENTlink modified 4 months ago by genomax62k • written 4 months ago by O.rka70

You can use mash (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x ), sourmash ( https://sourmash.readthedocs.io/en/latest/ ) or bbsketch.sh from BBMap suite (https://sourceforge.net/projects/bbmap/ ) can help you with the classification but I am not sure if they have functionality to extract those reads.

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax62k

https://github.com/will-rowe/hulk/ ?

ADD REPLYlink written 4 months ago by shenwei3564.5k
1
gravatar for genomax
4 months ago by
genomax62k
United States
genomax62k wrote:

cookiecutter (https://github.com/ad3002/Cookiecutter ) seems to do what you need. You will need to test and ascertain.

ADD COMMENTlink written 4 months ago by genomax62k

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

ADD REPLYlink written 4 months ago by O.rka70
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