What form of bacteria genome should we take for filtering

Question

[hirakuda]

https://www.ncbi.nlm.nih.gov/public/ In the above link there are many bacteria species. In genome category in singe bacteria folder there are many files. Which file I should use (i know some fasta or fastq file it should be) when I want to see the % of the bacteria in a filtered human sample?

[Carambakaracho]

Do you want to know about bacterial contamination of your otherwise pure human sample or is this about some microbiome? In either case, I fear there's no such thing like a single file.

[ATpoint]

Why do you think that there is bacterial contamination? Do you have low mapping rates for your sample?