--input r1.fq r2.fq i1.fq --read-structures 5M5S65T 75T 8B
For more information on read structures see: https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures
The same number of input files and read structures must be provided, with one exception: if supplying exactly 1 or 2 fastq files, both of which are solely template reads, no read structures need be provided.