The paired reads must be a match for the R1(forward) and R2(reverse) input to use Bowtie2 or Trinity.
During your processing, if one read from a pair was filtered out with BLASTN (determined to be contamination) you will also need to filter out the other read from the pair before continuing.
Other tools (besides Trimmomatic) that can create paired fastq output.
-
FastQ Interlacerfollowed byFastQ Deinterlacer