Show-diff outputs a list of structural differences for each sequence in the reference and query, sorted by position. For a reference sequence R, and its matching query sequence Q, differences are categorized as GAP (gap between two mutually consistent alignments), DUP (inserted duplication), BRK (other inserted sequence), JMP (rearrangement), INV (rearrangement with inversion), SEQ (rearrangement with another sequence). The first five columns of the output are seq ID, feature type, feature start, feature end, and feature length. Additional columns are added depending on the feature type. Negative feature lengths indicate overlapping adjacent alignment blocks
Parent program: MUMmer
MUMmer or 'Maximal Unique Matches' is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure and is one of the fastest and most efficient systems available for this task, enabling it to be applied to very long sequences. It has been widely used for comparing different genomes to one another. In recent years it has become a popular algorithm for comparing genome assemblies to one another, which allows scientists to determine how a genome has changed after adding more DNA sequence or after running a different genome assembly program.