Once a read has been mapped, a filtering process determines whether this match is good enough for the read to be included in the result. The filtering threshold is determined by two fractions:
- Length fraction
- The minimum length fraction of a read that must match the reference sequence. Setting a value at 0.5 means that at least half the read needs to match the reference sequence for the read to be included in the final mapping. This is set using the `-l' option. The default value is 0.5.
- The minimum fraction of identity between the read and the reference sequence. If you want the reads to have e.g. at least 90% identity with the reference sequence in order to be included in the final mapping, set this value to 0.9. Note that the similarity fraction does not apply to the whole read; it relates to the Length fraction. So with a length fraction set to 0.5, entering 0.9 for the similarity level has the meaning that at least 50 % of the read must have at least 90 % identity. This is set using the `-s' option. The default value is 0.8.