Use bam files of paired and unpaired (orphaned) reads

Can I use sorted bam files, which mapped both paired and unpaired (orphaned) reads onto my assembly?

I have many unpaired forward short reads, where the reverse reads didn't pass QC. It's a sequencing issue, alas. BUT, I would like to include these orphaned forward reads in any way I can because my coverage is already not great.

Contigs were assembled with metaSPAdes using both paired and unpaired simultaneously. Mapping was done with bowtie2, which also takes in both inputs. Its output reports statistics on paired and unpaired reads in two separate categories.

Using orphaned reads doubles my coverage in many samples, and this should help contig co-occurrence calculations in metabat2.

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