*2.3.3. Low-quality reads*

Apart from the cross-mapping ones, there are reads that can be generally considered as noise. The obvious ones are reads that are too short; excluding reads shorter than 90 bps will dramatically increase typing reliability [32]. With current sequencing technologies, it is possible to gain average read length much higher that 200 bps, but the low end of the read length distribution still should be excluded, especially when using enzymatic tagmentation [34].

#### *2.3.4. Random artifact reads*

Some reads do not map to our reference at all (off-target reads), or are not similar to any other reads in the data: if the ratio of these "orphan" reads is too high (the threshold can be set as a quality check metric), the resulting typing have to be treated with caution, particularly for homozygous cases in deep sequencing. If the typing/assembly algorithm is not prepared for random noise elimination, it can assemble bogus consensus sequences from noisy reads and present it as a candidate.
