When samples are small with fewer reads, for example, 100,000 reads, the default sourmash gather threshold of 50,000 bp might be too small to produce any results. It might be better to automatically adjust this threshold based on read depth of sample.
In addition, the filtering code might filter most, if not all sourmash results. The code should turn off the filtering automatically for smaller samples.
When samples are small with fewer reads, for example, 100,000 reads, the default sourmash gather threshold of 50,000 bp might be too small to produce any results. It might be better to automatically adjust this threshold based on read depth of sample.
In addition, the filtering code might filter most, if not all sourmash results. The code should turn off the filtering automatically for smaller samples.