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Microbial-Ecology-Group / AMRplusplus

AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.
https://www.meglab.org/
GNU General Public License v3.0
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Why is chr21 chosen for human read removal? #14

Closed tjdallman closed 1 year ago

tjdallman commented 1 year ago

Hello, I am wondering why chr21 is chosen for human read removal by default and not the whole genome e.g. GRCh38? Many thanks, Tim

EnriqueDoster commented 1 year ago

Hi Tim,

Ch21 is only used as an example fasta file to avoid including larger files in the repository. I would recommend running AMR++ with the entire genome as you mentioned.

Thanks!