nucmer is for the all-vs-all comparison of nucleotide sequences contained in multi-FastA data files. It is best used for highly similar sequence that may have large rearrangements. Common use cases are: comparing two unfinished shotgun sequencing assemblies, mapping an unfinished sequencing assembly to a finished genome, and comparing two fairly similar genomes that may have large rearrangements and duplications.

All output coordinates reference the forward strand of the involved sequence, regardless of the match direction. Also, nucmer now uses only matches that are unique in the reference sequence by default, use different Anchoring options to change this behavior.

Options::

Defaults in parentheses

nucmer

--sam-long      The original output format of nucmer, the delta format, contains only the minimum information necessary to quickly recreate the alignment.
It contains the name of the matching sequences, the length of the match, number of errors and positions of indels.
With --sam-long, it additionally reports the MD string (which specifies the mismatching positions), the sequence and, if applicable,
the quality values of the matching sequence. The long format is more expensive to compute and it generates larger output files,
but this option allows nucmer4 to match the behavior of other aligners such as Bowtie2 or BWA.

--mum             Use anchor matches that are unique in both the reference and query (false)

--maxmatch        Use all anchor matches regardless of their uniqueness (false)

-b                Set the distance an alignment extension will attempt to extend poor scoring regions
                  before giving up (200)

-c                Sets the minimum length of a cluster of matches (65)

-D                Set the maximum diagonal difference between two adjacent anchors in a cluster (5)

-d                Set the maximum diagonal difference between two adjacent anchors in a cluster as a
                  differential fraction of the gap length (0.12)

--noextend        Do not perform cluster extension step (false)

-f                Use only the forward strand of the Query sequences (false)

-r                Use only the reverse complement of the Query sequences (false)

-g                Set the maximum gap between two adjacent matches in a cluster (90)

-l                Set the minimum length of a single exact match (20)

-L                Minimum length of an alignment, after clustering and extension (0)

--nooptimize      No alignment score optimization, i.e. if an alignment extension reaches the end of a
                  sequence, it will not backtrack to optimize the alignment score and instead terminate
                  the alignment at the end of the sequence (false)

--nosimplify      Don't simplify alignments by removing shadowed clusters. Use this option when aligning
                  a sequence to itself to look for repeats (false)

--banded          Enforce absolute banding of dynamic programming matrix based on diagdiff parameter (false)

--large           Force the use of large offsets (false)

-G                Map genome to genome (long query sequences) (false)

-M                Max chunk. Stop adding sequence for a thread if more than MAX already. (50000)

mummerplot

-b             Highlight alignments with breakpoints further than breaklen nucleotides from the nearest
               sequence end

-color         Color plot lines with a percent similarity gradient or turn off all plot color (default
               color by match dir) If the plot is very sparse, edit the .gp script to plot with
               'linespoints' instead of 'lines'

-c             Generate a reference coverage plot (default for .tiling)

--filter       Only display .delta alignments which represent the "best" hit to any particular spot on
               either sequence, i.e. a one-to-one mapping of reference and query subsequences

--fat          Layout sequences using fattest alignment only

-IdR           Plot a particular reference sequence ID on the X-axis

-IdQ           Plot a particular query sequence ID on the Y-axis

-s             Set the output size to small, medium or large (--small) (--medium) (--large) (default 'small')

--SNP          Highlight SNP locations in each alignment

-title         Specify the gnuplot plot title (default none)

-x             Set the xrange for the plot '[min:max]'

-y             Set the yrange for the plot '[min:max]'

-R             Plot an ordered set of reference sequences from Rfile

-Q             Plot an ordered set of query sequences from Qfile

--layout       Layout a .delta multiplot in an intelligible fashion, this option requires the -R -Q options