Error in number of mapped fragments

[eric-kernfeld-dzd]

This is a quick interpretation question, which may reveal problems with the output depending on what you intend to estimate. In your paper describing fastANI, you write "At the end of the Mashmap run, all the query fragments are mapped to [the reference] B. The results are saved in a set M containing triplets of the form〈f, i, p〉, where f is the fragment id, i is the identity estimate, and p is the starting position where f is mapped to B."

In the example output, you show only 1303 out of 1608 mapped, not all. Similar results can be found by running the tool on simple test sequences. So:

• In cases where 1303/1608 fragments are mapped, is the output of the tool as intended?
• In cases where 1303/1608 fragments are mapped, is the size of the set M 1303, or 1608?

Thank you!

[cjain7]

We look for reciprocal best matches computed through forward and reverse searches. In the above example, there are 1303 reciprocal (bi-directional) best matches. Rationale for this bi-directional approach is to bound the ANI computation to orthologous genes and discard the paralogs.

1608 should be the count of query fragments (|A|/l in terms of notations in the paper). A subset of these contribute to bi-directional best matches.