Appropriate parameters for target enrichment antimicrobial resistance(AMR) Metagenomics

[Former user]

Dear all

I use this software to find AMR gene in multiplex PCR target enrichment antimicrobial resistance(AMR) Metagenomics, the ref sequences in each region may just have one base different. Some times I got inconsistent result from two regions of one AMR gene in one bacterial sample, the sample just have one pure bacteria. I want ask for help, what are the appropriate parameters in this situation.

Thank you all.

[li chen]

I use this command: $kma  -ex_mode -1t1 -vcf -sam -cge -ipe $R1fq $R2fq -t ${threads} -t_db $db -o $outdir/${i}.kma  > $outdir/${i}.sam