MUMMER(1)

📦 version 3.23, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ MUMMER(1) — General Commands Manual ✨

okay bestie, welcome to mummer(1) 💖 this is the General Commands Manual page for the whole mummer package — a whole lil family of tools that do sequence alignment of multiple genomes. it's a big one so buckle up, we're doing this in parts 🫶

🌸 NAME 🌸

mummer — package for sequence alignment of multiple genomes 🧬✨

💅 SYNOPSIS 💅

mummer-annotate <gapfile><datafile>
combineMUMs <RefSequence><MatchSequences><GapsFile>
dnadiff [options]<reference><query> or [options]-d<deltafile>
exact-tandems <file><min-match-len>
gaps
mapview [options]<coordsfile>[UTRcoords][CDScoords]
mgaps [-d<DiagDiff>][-f<DiagFactor>][-l<MatchLen>][-s<MaxSeparation>]
mummer [options]<reference-file><query-files>
mummerplot [options]<matchfile>
nucmer [options]<Reference><Query>
nucmer2xfig
promer [options]<Reference><Query>
repeat-match [options]<genome-file>
run-mummer1 <fastareference><fastaquery><prefix>[-r]
run-mummer3 <fastareference><multi-fastaquery><prefix>
show-aligns [options]<deltafile><refID><qryID>

so like, the input here is the .delta output of either the nucmer program or the promer program, and you pass it right on the command line 🎀

the output goes to stdout, and it's made up of all the alignments between the query and reference sequences you named on the command line. all of them. every single one. no skimping 💯

⚠️ NOTE: no sorting is done by default, so the alignments will be ordered exactly as they're found in the <deltafile> input. it's giving "first come first served" and honestly? iconic.
show-coords [options]<deltafile>
show-snps [options]<deltafile>
show-tiling [options]<deltafile>

🦋 DESCRIPTION 🦋

this section is just vibes and honestly it's empty in the original too, so we move 🙈

👑 OPTIONS 👑

okay so all the tools — except for gaps — obey the -h, --help, -V and --version options, exactly as one would expect. and bestie, this help is excellent, it makes these man pages basically obsolete. i said what i said 💅

🍓 combineMUMs 🍓

combines MUMs in <GapsFile> by extending matches off ends and between MUMs ✨

  • <RefSequence> is a fasta file of the reference sequence
  • <MatchSequences> is a multi-fasta file of the sequences matched against the reference

the flags, in order:

  • -D — only output to stdout the difference positions and characters
  • -n — allow matches only between nucleotides, i.e., ACGTs
  • -N num — break matches at <num> or more consecutive non-ACGTs
  • -q tag — used to label query match
  • -r tag — used to label reference match
  • -S — output all differences in strings
  • -t — label query matches with query fasta header
  • -v num — set verbose level for extra output
  • -W file — reset the default output filename witherrors.gaps
  • -x — don't output .cover files
  • -e — set error-rate cutoff to e (e.g. 0.02 is two percent)

🌈 dnadiff 🌈

runs comparative analysis of two sequence sets using nucmer and its associated utilities with recommended parameters 🔥 see the MUMmer documentation for a more detailed description of the output.

it produces the following output files:

  • .report — summary of alignments, differences and SNPs
  • .delta — standard nucmer alignment output
  • .1delta — 1-to-1 alignment from delta-filter -1
  • .mdelta — M-to-M alignment from delta-filter -m
  • .1coords — 1-to-1 coordinates from show-coords -THrcl .1delta
  • .mcoords — M-to-M coordinates from show-coords -THrcl .mdelta
  • .snps — SNPs from show-snps -rlTHC .1delta
  • .rdiff — classified ref breakpoints from show-diff -rH .mdelta
  • .qdiff — classified qry breakpoints from show-diff -qH .mdelta
  • .unref — unaligned reference IDs and lengths (if applicable)
  • .unqry — unaligned query IDs and lengths (if applicable)

💖 MANDATORY:

  • reference — set the input reference multi-FASTA filename
  • query — set the input query multi-FASTA filename
  • or
  • delta file — unfiltered .delta alignment file from nucmer

💖 OPTIONS:

  • -d|delta — provide precomputed delta file for analysis
  • -h
  • --help — display help information and exit
  • -p|prefix — set the prefix of the output files (default "out")
  • -V
  • --version — display the version information and exit

🧚 mapview 🧚

  • -h
  • --help — display help information and exit
  • -m|mag — set the magnification at which the figure is rendered, this is an option for fig2dev which is used to generate the PDF and PS files (default 1.0)
  • -n|num — set the number of output files used to partition the output, this is to avoid generating files that are too large to display (default 10)
  • -p|prefix — set the output file prefix (default "PROMER_graph or NUCMER_graph")
  • -v
  • --verbose — verbose logging of the processed files
  • -V
  • --version — display the version information and exit
  • -x1 coord — set the lower coordinate bound of the display
  • -x2 coord — set the upper coordinate bound of the display
  • -g|ref — if the input file is provided by mgaps, set the reference sequence ID (as it appears in the first column of the UTR/CDS coords file)
  • -I — display the name of query sequences
  • -Ir — display the name of reference genes

💜 mummer 💜

finds and outputs (to stdout) the positions and length of all sufficiently long maximal matches of a substring in <query-file> and <reference-file> 🎯

  • -mum — compute maximal matches that are unique in both sequences
  • -mumcand — same as -mumreference
  • -mumreference — compute maximal matches that are unique in the reference-sequence but not necessarily in the query-sequence (default)
  • -maxmatch — compute all maximal matches regardless of their uniqueness
  • -n — match only the characters a, c, g, or t; they can be in upper or in lower case
  • -l — set the minimum length of a match; if not set, the default value is 20
  • -b — compute forward and reverse complement matches
  • -r — only compute reverse complement matches
  • -s — show the matching substrings
  • -c — report the query-position of a reverse complement match relative to the original query sequence
  • -F — force 4 column output format regardless of the number of reference sequence inputs
  • -L — show the length of the query sequences on the header line

✨ nucmer ✨

nucmer generates nucleotide alignments between two mutli-FASTA input files. two output files are generated:

  • the .cluster output file lists clusters of matches between each sequence
  • the .delta file lists the distance between insertions and deletions that produce maximal scoring alignments between each sequence

🎀 MANDATORY:

  • Reference — set the input reference multi-FASTA filename
  • Query — set the input query multi-FASTA filename

🎀 OPTIONS:

  • --mum — use anchor matches that are unique in both the reference and query
  • --mumcand — same as --mumreference
  • --mumreference — use anchor matches that are unique in in the reference but not necessarily unique in the query (default behavior)
  • --maxmatch — use all anchor matches regardless of their uniqueness
  • -b|breaklen — set the distance an alignment extension will attempt to extend poor scoring regions before giving up (default 200)
  • -c|mincluster — sets the minimum length of a cluster of matches (default 65)
  • --[no]delta — toggle the creation of the delta file (default --delta)
  • --depend — print the dependency information and exit
  • -d|diagfactor — set the clustering diagonal difference separation factor (default 0.12)
  • --[no]extend — toggle the cluster extension step (default --extend)
  • -f
  • --forward — use only the forward strand of the Query sequences
  • -g|maxgap — set the maximum gap between two adjacent matches in a cluster (default 90)
  • -h
  • --help — display help information and exit
  • -l|minmatch — set the minimum length of a single match (default 20)
  • -o
  • --coords — automatically generate the original NUCmer1.1 coords output file using the show-coords program
  • --[no]optimize — toggle alignment score optimization, i.e. if an alignment extension reaches the end of a sequence, it will backtrack to optimize the alignment score instead of terminating the alignment at the end of the sequence (default --optimize)
  • -p|prefix — set the prefix of the output files (default "out")
  • -r
  • --reverse — use only the reverse complement of the Query sequences
  • --[no]simplify — simplify alignments by removing shadowed clusters. turn this option off if aligning a sequence to itself to look for repeats (default --simplify)

🌟 promer 🌟

promer generates amino acid alignments between two mutli-FASTA DNA input files. two output files are generated:

  • the .cluster output file lists clusters of matches between each sequence
  • the .delta file lists the distance between insertions and deletions that produce maximal scoring alignments between each sequence

the DNA input is translated into all 6 reading frames in order to generate the output, but the output coordinates reference the original DNA input 👑

🦄 MANDATORY:

  • Reference — set the input reference multi-FASTA DNA file
  • Query — set the input query multi-FASTA DNA file

🦄 OPTIONS:

  • --mum — use anchor matches that are unique in both the reference and query
  • --mumcand — same as --mumreference
  • --mumreference — use anchor matches that are unique in in the reference but not necessarily unique in the query (default behavior)
  • --maxmatch — use all anchor matches regardless of their uniqueness

okay bestie we're still in the options, I know, but the mummer flag buffet is nearly done, stay with me 💖

  • -b|breaklen — how far an alignment extension will try to push through a poorly-scoring region before it gives up, measured in amino acids (default 60)
  • -c|mincluster — the minimum length of a cluster of matches, measured in amino acids (default 20)
  • --[no]delta — toggles whether the delta file gets made at all (default --delta)
  • --depend — prints the dependency info and then dips ✌️
  • -d|diagfactor — the clustering diagonal difference separation factor (default .11)
  • --[no]extend — toggles the cluster extension step (default --extend)
  • -g|maxgap — the biggest gap allowed between two adjacent matches inside a cluster, measured in amino acids (default 30)
  • -l|minmatch — the minimum length of a single match, measured in amino acids (default 6)
  • -m|masklen — the maximum bookend masking length, measured in amino acids (default 8)
  • -o, --coords — automatically generates the original PROmer1.1 .coords output file using the show-coords program
  • --[no]optimize — toggles alignment score optimization. like, if an alignment extension reaches the end of a sequence, it'll backtrack to optimize the alignment score instead of just terminating the alignment at the end of the sequence (default --optimize)
  • -p|prefix — sets the prefix of the output files (default "out")
  • -x|matrix — picks the alignment matrix number: 1 [BLOSUM 45], 2 [BLOSUM 62] or 3 [BLOSUM 80] (default 2)

🎀 repeat-match 🎀

finds all the maximal exact matches in <genome-file> — no notes, just vibes 🦋

  • -E — use exhaustive (slow) search to find matches. bestie, it's thorough but it's slow, you've been warned 🐌
  • -f — forward strand only, don't use the reverse complement
  • -n # — set minimum exact match length to #
  • -t — only output tandem repeats
  • -V # — set the level of verbose (debugging) printing to #

✨ show-aligns ✨

  • -h — display help information
  • -q — sort alignments by the query start coordinate
  • -r — sort alignments by the reference start coordinate
  • -w int — set the screen width — default is 60
  • -x int — set the matrix type — default is 2 (BLOSUM 62), other options include 1 (BLOSUM 45) and 3 (BLOSUM 80)
    • note: only has effect on amino acid alignments

💅 show-coords 💅

  • -b — merges overlapping alignments regardless of match dir or frame, and does not display any identity information
  • -B — switch output to btab format
  • -c — include percent coverage information in the output
  • -d — display the alignment direction in the additional FRM columns (default for promer)
  • -g — deprecated option. Please use 'delta-filter' instead
  • -h — display help information
  • -H — do not print the output header
  • -I float — set minimum percent identity to display
  • -k — knockout (do not display) alignments that overlap another alignment in a different frame by more than 50% of their length, AND have a smaller percent similarity or are less than 75% of the size of the other alignment (promer only)
  • -l — include the sequence length information in the output
  • -L long — set minimum alignment length to display
  • -o — annotate maximal alignments between two sequences, i.e. overlaps between reference and query sequences
  • -q — sort output lines by query IDs and coordinates
  • -r — sort output lines by reference IDs and coordinates
  • -T — switch output to tab-delimited format

Input is the .delta output of either the nucmer or the promer program passed on the command line.

Output is to stdout, and it's a list of coordinates, percent identity, and other useful info about the alignment data sitting in the .delta file you fed it as input.

NOTE: no sorting is done by default, so the alignments will be ordered exactly as found in the <deltafile> input. fr fr, no sneaky reordering 🌸

🫶 show-snps 🫶

  • -C — do not report SNPs from alignments with an ambiguous mapping, i.e. only report SNPs where the [R] and [Q] columns equal 0 and do not output these columns
  • -h — display help information
  • -H — do not print the output header
  • -I — do not report indels
  • -l — include sequence length information in the output
  • -q — sort output lines by query IDs and SNP positions
  • -r — sort output lines by reference IDs and SNP positions
  • -S — specify which alignments to report by passing 'show-coords' lines to stdin
  • -T — switch to tab-delimited format
  • -x int — include x characters of surrounding SNP context in the output, default 0

Input is the .delta output of either the nucmer or promer program passed on the command line.

Output is to stdout, and it's a list of SNPs (or amino acid substitutions for promer) with positions and other useful info. Output will be sorted with -r by default, and the [BUFF] column will always refer to the sequence whose positions have been sorted. That value is the distance from this SNP to the nearest mismatch (end of alignment, indel, SNP, etc) in the same alignment, while the [DIST] column is the distance from this SNP to the nearest sequence end. SNPs where the [R] and [Q] columns are greater than 0 should be evaluated with caution, because those columns specify the number of other alignments overlapping this position. Use -C to make sure SNPs are only reported from unique alignment regions. protect your peace and your SNP calls 💜

🌈 show-tiling 🌈

  • -a — describe the tiling path by printing the tab-delimited alignment region coordinates to stdout
  • -c — assume the reference sequences are circular, and allow tiled contigs to span the origin
  • -g int — set maximum gap between clustered alignments [-1, INT_MAX]
    • a value of -1 will represent infinity
    • (nucmer default = 1000)
    • (promer default = -1)
  • -i float — set minimum percent identity to tile [0.0, 100.0]
    • (nucmer default = 90.0)
    • (promer default = 55.0)
  • -l int — set minimum length contig to report [-1, INT_MAX]
    • a value of -1 will represent infinity
    • (common default = 1)
  • -p file — output a pseudo molecule of the query contigs to 'file'
  • -R — deal with repetitive contigs by randomly placing them in one of their copy locations (implies -V 0)
  • -t file — output a TIGR style contig list of each query sequence that sufficiently matches the reference (non-circular)
  • -u file — output the tab-delimited alignment region coordinates of the unusable contigs to 'file'
  • -v float — set minimum contig coverage to tile [0.0, 100.0]
    • (nucmer default = 95.0) sum of individual alignments
    • (promer default = 50.0) extent of syntenic region
  • -V float — set minimum contig coverage difference [0.0, 100.0], i.e. the difference needed to determine one alignment is 'better' than another alignment
    • (nucmer default = 10.0) sum of individual alignments
    • (promer default = 30.0) extent of syntenic region
  • -x — describe the tiling path by printing the XML contig linking information to stdout

Input is the .delta output of the nucmer program, run on very similar sequence data, or the .delta output of the promer program, run on divergent sequence data.

Output is to stdout, and it's the predicted location of each aligning query contig as mapped to the reference sequences. These coordinates reference the extent of the entire query contig, even when only a certain percentage of the contig was actually aligned (unless the -a option is used). Columns are, start in ref, end in ref, distance to next contig, length of this contig, alignment coverage, identity, orientation, and ID respectively. 👑

🌟 SEE ALSO 🌟

http://mummer.sourceforge.net/

Open source MUMmer 3.0 is described in Versatile and open software for comparing large genomes. S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S.L. Salzberg, Genome Biology (2004), 5:R12.

💖 AUTHOR 💖

mummer was written by S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S.L. Salzberg.

and that's a wrap bestie, you made it to the end of MUMMER(1) 🎀 this whole icon of a manual page is dated May 21, 2005, and it's living in the MUMMER(1) section of your man pages — go forth and align something gorgeous, ily, no cap 🦋✨

📦 where this page comes from