A computer-implemented method for sequencing data read realignment, the method comprising: obtaining from a sequence alignment dataset an initial alignment of a read sequence to a reference sequence, the initial alignment comprising an aligned read; performing realignment processing on the initial alignment, the realignment processing realigning the read sequence to the reference sequence to produce one or more candidate realignments that are different from the initial alignment, and the realignment processing comprising: identifying one or more candidate indels, the one or more candidate indels comprising at least one indel in the aligned read and at least one indel aligned proximal to the aligned read as indicated by the sequence alignment dataset; creating a flattened aligned read based at least on removing from the aligned read any indels indicated by the initial alignment; and determining the one or more candidate realignments of the read sequence to the reference sequence based on introducing, for each candidate realignment of the one or more candidate realignments, a respective at least one candidate indel of the one or more candidate indels into the flattened aligned read; and providing the initial alignment or a selected candidate realignment of the one or more candidate realignments based on one or more selection criteria, wherein the one or more candidate indels comprise a plurality of candidate indels, and wherein the determining the one or more candidate realignments comprises commencing iteratively introducing the plurality of candidate indels into the flattened aligned read, wherein each iteration of the iteratively introducing provides a candidate realignment of the one or more candidate realignments by introducing into the flattened aligned read the respective at least one candidate indel for the candidate realignment. obtaining from a sequence alignment dataset an initial alignment of a read sequence to a reference sequence, the initial alignment comprising an aligned read; performing realignment processing on the initial alignment, the realignment processing realigning the read sequence to the reference sequence to produce one or more candidate realignments that are different from the initial alignment, and the realignment processing comprising: identifying one or more candidate indels, the one or more candidate indels comprising at least one indel in the aligned read and at least one indel aligned proximal to the aligned read as indicated by the sequence alignment dataset; creating a flattened aligned read based at least on removing from the aligned read any indels indicated by the initial alignment; and determining the one or more candidate realignments of the read sequence to the reference sequence based on introducing, for each candidate realignment of the one or more candidate realignments, a respective at least one candidate indel of the one or more candidate indels into the flattened aligned read; identifying one or more candidate indels, the one or more candidate indels comprising at least one indel in the aligned read and at least one indel aligned proximal to the aligned read as indicated by the sequence alignment dataset; creating a flattened aligned read based at least on removing from the aligned read any indels indicated by the initial alignment; and determining the one or more candidate realignments of the read sequence to the reference sequence based on introducing, for each candidate realignment of the one or more candidate realignments, a respective at least one candidate indel of the one or more candidate indels into the flattened aligned read; and providing the initial alignment or a selected candidate realignment of the one or more candidate realignments based on one or more selection criteria, wherein the one or more candidate indels comprise a plurality of candidate indels, and wherein the determining the one or more candidate realignments comprises commencing iteratively introducing the plurality of candidate indels into the flattened aligned read, wherein each iteration of the iteratively introducing provides a candidate realignment of the one or more candidate realignments by introducing into the flattened aligned read the respective at least one candidate indel for the candidate realignment.