Are paired and single end read files supported together?

[winni2k]

I would like to use reads from paired end sequencing that have been trimmed with trimmomatic and merged with pear. Both tools output two files for paired-end reads, and one file with reads that no longer have an associated second read due to trimming (trimmomatic) or due to merging (pear). Is there a way to do a joint kallisto analysis on all three files?