Illustration from Scientific Research

Alignment using minimap2 [63] is done to identify mismatches and breaks in coverage, which could be an indication of potential assembly error. (i) Low confidence positions are captured from a read view by collecting positions with >= 5 reads that have > 1% mismatch rate. (ii) Mismatch rate is calculated for every position, considering only mismatches occurred exactly at the given position ( basepair-oriented ). (iii) Coverage breaks are found by collecting positions with <= 2 reads mapped.

DOI