MetaPhlAn version 4.0.6 ( 1 Mar 2023)
command used: $ metaphlan sample1_1.fastq,sample1_2.fastq --bowtie2out sample1.bowtie2.bz2 --nproc 5 --input_type fastq > sample1_profiled_metagenome.txt
Greetings,
I’m working with metagenomic data and using MetaPhlAn for taxonomic profiling. While the tool provides the number of processed reads, I’m interested in determining the percentage of reads that were actually classified (i.e., successfully assigned to a taxon) in my metagenome samples. This information would be valuable for assessing the efficiency of the classification and the overall quality of my samples.
Is there a built-in way to obtain this information directly from MetaPhlAn’s output? If not, could you recommend the most accurate method to calculate or estimate this percentage using the available output files?
Thank you for your guidance on this matter.