Question: How to extract reads that match k-mer profiles from a collection of sequences?
0
gravatar for O.rka
14 months ago by
O.rka130
O.rka130 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 • 397 views
ADD COMMENTlink modified 14 months ago by genomax75k • written 14 months ago by O.rka130

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 14 months ago • written 14 months ago by genomax75k

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

ADD REPLYlink written 14 months ago by shenwei3565.0k
1
gravatar for genomax
14 months ago by
genomax75k
United States
genomax75k wrote:

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

ADD COMMENTlink written 14 months ago by genomax75k

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

ADD REPLYlink written 14 months ago by O.rka130
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