Since aligned reads contain insertions and deletions, we use placeholders I and D to simplify position referencing among the reads. All placeholders are treated as additional allele values but they are removed from the final assembled sequences. First, we substitute each deletion in the aligned reads with placeholder D. Deletion supported by a single read is replaced either with the allele value, which is present in all other reads overlapping this position, or with N, signifying an unknown value, otherwise. Next, we fill with placeholder I each gap in a read corresponding to the insertions in the other reads. All insertions supported by a single read are removed from consideration.