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.
Hi,
I am trying to extract the reads or read IDs from the BAM file. But would like to extract only those counted in the SNPconfirmed_deduped matrix output. My objective is to see which organisms are responsible for these reads.
I know that I could use Kraken output or generate MAGs and check. But is there any existing command in the AMR++ pipeline itself or a simple way to extract those?
Hi, I am trying to extract the reads or read IDs from the BAM file. But would like to extract only those counted in the SNPconfirmed_deduped matrix output. My objective is to see which organisms are responsible for these reads.
I know that I could use Kraken output or generate MAGs and check. But is there any existing command in the AMR++ pipeline itself or a simple way to extract those?
Please let me know.
Thank you