Show-coords

show-coords parses the delta alignment output of NUCmer and PROmer, and displays summary information such as position, percent identity and so on, of each alignment. It is the most commonly used tool for analyzing the delta files. Usually the -r is used to sort lines by reference

Show-tiling

show-tiling attempts to construct a tiling path out of the query contigs as mapped to the reference sequences. Given the delta alignment information of a few long reference sequences and many small query contigs, show-tiling will determine the best mapped location of each query contig. Note that each contig may only be tiled once, so repetitive regions may cause this program some difficulty. This program is useful for aiding in the scaffolding and closure of an unfinished set of contigs, if a suitable, high similarity reference genome is available. Or, if using PROmer, show-tiling will help in the identification of syntenic regions and their contig's mapping to the references.

This program is not suitable for "many vs. many" assembly comparisons, however a new tool based on the concepts of show-tiling should be available in the near future that will facilitate the mapping of assembly contigs.

Show-snps

show-snps is a utility program for reporting polymorphisms contained in a delta encoded alignment file output by NUCmer or PROmer. It catalogs all of the single nucleotide polymorphisms (SNPs) and insertions/deletions within the delta file alignments. Polymorphisms are reported one per line, in a delimited fashion similar to show-coords. Pairing this program with the appropriate MUMmer tools can create an easy to use SNP pipeline for the rapid identification of putative SNPs between any two sequence sets, as demonstrated in the manual SNP detection section.

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.

IDR GAP gap-start gap-end gap-length-R gap-length-Q gap-diff
IDR DUP dup-start dup-end dup-length
IDR BRK gap-start gap-end gap-length
IDR JMP gap-start gap-end gap-length
IDR INV gap-start gap-end gap-length
IDR SEQ gap-start gap-end gap-length prev-sequence next-sequence

Positions always reference the sequence with the given ID. The sum of the fifth column (ignoring negative values) is the total amount of inserted sequence. Summing the fifth column after removing DUP features is total unique inserted sequence. Note that unaligned sequence are not counted, and could represent additional "unique" sequences. See documentation for tips on how to interpret these alignment break features.

Show-aligns

show-aligns parses the delta encoded alignment output of NUCmer and PROmer, and displays the pair-wise alignments from the two sequences specified on the command line. It is handy for identifying the exact location of errors and looking for SNPs between two sequences.

Delta-filter

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.