Do I need to run kneaddata first before running raw shotgun files in metaphlan?

Microbial community profiling MetaPhlAn
1

I am just getting started to use metaphlan. Do I have to run kneaddata first to remove human sequences? I did not see this anywhere in the tutorial.

Thanks!

2

I recommend you check papers and methodologies to see how they process the data, I suggest first removing adapters and then running Kneaddata before use metaphlan, greetings

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3

Thanks! Will do! What do you like to use to remove adapters?

4

Trimmomatic is a good option

5

Not if you begin by read alignment to another species. For example, if human cancer whole genome sequencing was performed, the first step would have been to map to a human reference genome such as hg38 because the primary interest for the data is probably somatic variants. Then, the host DNA has already been removed. It is unlikely that adapter trimming would be important unless the DNA was excessively fragmented and the insert size therefore was small.

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