A method for designing barcode sequences corresponding to flowspace codewords, comprising: generating a plurality of flowspace codewords, the codewords comprising a string of characters; determining a location for at least one padding character within the flowspace codewords by moving the padding character such that it is not at the terminating flow of a codeword and the corresponding padding base is not the terminating base of a barcode sequence; inserting the padding character into the flowspace codewords at the determined location, wherein the determined location of the padding character prevents two successive incorporations of a same base in the predetermined flow order with no other base incorporation in between and wherein determining a location for the padding character within the flowspace codewords further comprises: iterating over a plurality of locations for the padding character within the codewords; for each iteration, calculating a number of codewords that correspond to a valid base space sequence according to the predetermined flow order; and selecting the location of the plurality of locations with the highest calculated number of codewords that correspond to a valid base space sequence, selecting, after the inserting, a plurality of the flowspace codewords based on satisfying a predetermined minimum distance criteria, wherein the selected codewords correspond to valid base space sequences according to a predetermined flow order, wherein a valid base space sequence corresponds to a possible nucleic acid sequence in a base space given the predetermined flow order; and manufacturing the barcode sequences corresponding to the selected codewords. generating a plurality of flowspace codewords, the codewords comprising a string of characters; determining a location for at least one padding character within the flowspace codewords by moving the padding character such that it is not at the terminating flow of a codeword and the corresponding padding base is not the terminating base of a barcode sequence; inserting the padding character into the flowspace codewords at the determined location, wherein the determined location of the padding character prevents two successive incorporations of a same base in the predetermined flow order with no other base incorporation in between and wherein determining a location for the padding character within the flowspace codewords further comprises: iterating over a plurality of locations for the padding character within the codewords; for each iteration, calculating a number of codewords that correspond to a valid base space sequence according to the predetermined flow order; and selecting the location of the plurality of locations with the highest calculated number of codewords that correspond to a valid base space sequence, selecting, after the inserting, a plurality of the flowspace codewords based on satisfying a predetermined minimum distance criteria, wherein the selected codewords correspond to valid base space sequences according to a predetermined flow order, wherein a valid base space sequence corresponds to a possible nucleic acid sequence in a base space given the predetermined flow order; and manufacturing the barcode sequences corresponding to the selected codewords. iterating over a plurality of locations for the padding character within the codewords; for each iteration, calculating a number of codewords that correspond to a valid base space sequence according to the predetermined flow order; and selecting the location of the plurality of locations with the highest calculated number of codewords that correspond to a valid base space sequence, selecting, after the inserting, a plurality of the flowspace codewords based on satisfying a predetermined minimum distance criteria, wherein the selected codewords correspond to valid base space sequences according to a predetermined flow order, wherein a valid base space sequence corresponds to a possible nucleic acid sequence in a base space given the predetermined flow order; and manufacturing the barcode sequences corresponding to the selected codewords.