Delta-filter is a utility program for the manipulation of the delta encoded alignment files output by the NUCmer and PROmer pipelines. It takes a delta file as input and filters the information based on the various command line switches, outputting only the desired alignments to stdout. Options to filter by alignment length, identity, uniqueness and consistency are provided. Certain combinations of these options can greatly reduce the number of unwanted alignments in the delta file, thus making the output of programs such as show-coords more comprehendible. What is delta file? The delta file is a representation of the all-vs-all alignment between the sequences contained in the multi-FASTA input files. It catalogs the coordinates of aligned regions and the distance between insertions and deletions contained in these alignment regions.
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.