Failed to identify identical 150 bp read

[Former user]

Hi,

I'm having trouble KMA v1.3.14 on a simple test set. I am building an index as follows:

kma index -i ref.fna -o db

And then mapping reads with:

kma -i reads.fna -o kma_results -t_db db

The reads.fna file contains two 150 bp read that are both 100% identical to a region in the single reference sequence in ref.fna. However, KMA returns no mapping results. I have attached the test files. Any reason why KMA might fail to report a mapping? Some sort of complexity filtering?

Thanks, Donovan

[ptlcc]

Hi Donovan

There were an error for databases with only one sequence, it has been fixed from v1.3.14a.

You should add the option “-ID 0.0“ for this test, as the reads covers < 1% of the reference.

Best,
Philip