Paired-read awareness of MEGAN


On the page 44 of User Manual for MEGAN V6.4.12, you indicted there is a option to select input data as paired-read (see blow),

The Paired Reads item is used to turn paired-read awareness of MEGAN on and off. In paired read mode, MEGAN utilities read-pairing information to enhance the taxonomic assignment of reads.

But actually in the MEGAN V6.4.15, there is no such option (see screenshot).

Would you take a look? thanks,


Dear Gary,

The paired reads option in the middle of the files tab, I will update the manual accordingly…


Thanks, but paired reads option is not in the Meganize DAA file page, since i ran the diamond first.


The meganizer feature currently does not support paired-reads processing.

Moreover, it is unclear how well the way that MEGAN currently handles paired reads works in practice.
MEGAN currently does the follows:
if there are any taxa to which both reads have a significant alignment, then MEGAN assigns both reads to the LCA of those common taxa. If only one read has significant alignments to any taxa, then both reads are assigned to the LCA of those taxa. Otherwise, both reads are assigned independently.
There is no special handling of paired reads in functional classification.
The assignments made in this way sometimes look suspicious and thus we looking into ways of improving this.