Systems, methods, and computer-readable storage media are provided reconstructing barcode signals utilizing sequence alignment matrices. A barcode signal is received that is associated with a portion of a barcode symbol and includes a sequence of bar elements and space elements in alternating order. A sequence alignment matrix (SAM) is built such that each row represents an element of an already reconstructed portion of the barcode symbol, each column represents an element of the received barcode signal sequence, and the potential alignments are placed on a plurality of diagonals thereof. A score is assigned to each matrix square that includes an element of the received barcode signal sequence and a diagonal score is calculated for each of the plurality of diagonals by summing the scores for each matrix square respectively comprising each of the plurality of diagonals.