Filtering on Query coverage


Hello everyone
I would like to apply a filter on query coverage. There would be a simple way to realize this filtering out of MALT for example.


The latest release of MEGAN has a “Min Percent Read to Cover” item in the Options->LCA Parameters dialog, Advanced tab. You could perform binning with a threshold set to 90%, say, then only reads with at leaset 90% coverage will be assigned to taxa, the others will go to the Unassigned node.
Then select all nodes except the Unassigned node and “Extract Reads” for those nodes.
Then you will have the reads that have 90% or more coverage.

Note that the “Min Percent Read to Cover” item performs slightly differently, depending whether you are in long read mode or not. If not in long read, i.e., if in short read mode (the default), read coverage is based on the longest alignment found for a read. So, in theory, if a read has two short alignments, side by side, then the coverage will be based on one of them, not on their union. This is for perform reasons.
In long read mode, coverage reflects the number of bases covered by any of the read’s alignments, which takes longer to calculate, but is necessary, of course, for long reads.


yes I used the Advanced tab with “min percent read to cover” at 0.1 or 0.5.


Hi Daniel,
I am not sure how to use the advanced option “Min Percent Read to Cover” item in the Options-> LCA Parameters dialog, Advanced tab. (MEGAN 6.8.5 window).

I only get assigned reads has a threshold value of min coverage of 0.1 ???

If I set this parameter to 0.3 no reads were assigned however some should be (see figure2)
1/ Do the MALT output need to specify a particular format option? (I used MALT default parameter)
2/ From what size should a read be considered long?

Below the parameters used :

Sequence for which a hit should be kept with a min coverage of 0.5:

thank you for your help




Your screen-shot shows the Parameters tab, not the Advanced tab, are you using the Advanced tab?


yes I used the Advanced tab with “min percent read to cover” at 0.1 or 0.5.