Paired end fastq files as input for PanPhlAn

Microbial community profiling PanPhlAn
1

Hello,
I have paired-end samples. How should I use panphlan_map.py -i with my two files/sample (sample1_R1 and sample1_R2)?

Thank you very much,

Sara

2

Hello,

you should use a concatenation of both files as input. Even three if you have some file with unpaired (UN) reads.

Have a good day
Léonard

3

Thank you very much, Léonard