Find contamination in database

Nanopore_newbie

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Join Date: Sep 2021

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#1

Find contamination in database

09-21-2021, 12:22 AM

Hi everyone.

I'm quite new to NGS and is currently working on creating a custom database of reference genomes.
I want to check if theres any human contamination in the database and therefore I'm trying to map the database to the human genome (GRCh38).

As I understand it, i have to create pseudoreads/contigs from each genome in my database before I can map them to the human genome.
Is that the right way to proceed? And if so, is there a smart way of doing this?

Any help is really appreciated
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GenoMax

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Join Date: Feb 2008

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#2

09-21-2021, 05:24 AM

You could use "minimap2" to align against the human genome. That said you will need to be judicious about results as you determine what is "human" contamination. Depending on the genomes you are working with there can be sequence similarities.

There are other aligners like "lastz" that can align chromosome sized sequences as well.
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