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mummer

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mummer: package for sequence alignment of multiple genomes

NAME
mummer - package for sequence alignment of multiple genomes

SYNOPSIS

mummer-annotate <gapfile><datafile> combineMUMs <RefSequence><MatchSequences><GapsFile> delta-filter [options]<deltafile> 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> Input is the .delta output of either the "nucmer" or the "promer" program passed on the command line. Output is to stdout, and consists of all the alignments between the query and reference sequences identified on the command line. NOTE: No sorting is done by default, therefore the alignments will be ordered as found in the <deltafile> input. show-coords [options]<deltafile> show-snps [options]<deltafile> show-tiling [options]<deltafile>

DESCRIPTION

OPTIONS

All tools (exept for gaps) obey to the -h, --help, -V and --version options as one would expect. This help is excellent and makes these man pages basically obsolete. 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 -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 Run comparative analysis of two sequence sets using nucmer and its associated utilities with recommended parameters. See MUMmer documentation for a more detailed description of the output. 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 delta-filter -e float For switches -g -r -q, keep repeats within e percent of the best LIS score [0, 100], no repeats by default -g Global alignment using length*identity weighted LIS. For every reference-query pair, leave only the aligns which form the longest mutually consistent set -h Display help information -i float Set the minimum alignment identity [0, 100], default 0 -l int Set the minimum alignment length, default 0 -q Query alignment using length*identity weighted LIS. For each query, leave only the aligns which form the longest consistent set for the query -r Reference alignment using length*identity weighted LIS. For each reference, leave only the aligns which form the longest consistent set for the reference -u float Set the minimum alignment uniqueness, i.e. percent of the alignment matching to unique reference AND query sequence [0, 100], default 0 -o float Set the maximum alignment overlap for -r and -q options as a percent of the alignment length [0, 100], default 100 Reads a delta alignment file from either nucmer or promer and filters the alignments based on the command-line switches, leaving only the desired alignments which are output to stdout in the same delta format as the input. For multiple switches, order of operations is as follows: -i -l -u -q -r -g. If an alignment is excluded by a preceding operation, it will be ignored by the succeeding operations An important distinction between the -g option and the -r -q options is that -g requires the alignments to be mutually consistent in their order, while the -r -q options are not required to be mutually consistent and therefore tolerate translocations, inversions, etc. Thus, -r provides a one-to-many, -q a many-to-one, -r -q a one-to-one local mapping, and -g a one-to-one global mapping of reference and query bases respectively. 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 Find and output (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 nuncmer 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 --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 --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, measured in amino acids (default 60) -c|mincluster Sets the minimum length of a cluster of matches, measured in amino acids (default 20) --[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 .11) --[no]extend Toggle the cluster extension step (default --extend) -g|maxgap Set the maximum gap between two adjacent matches in a cluster, measured in amino acids (default 30) -l|minmatch Set the minimum length of a single match, measured in amino acids (default 6) -m|masklen Set the maximum bookend masking lenth, measured in amino acids (default 8) -o --coords Automatically generate the original PROmer1.1 ".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") -x|matrix Set the alignment matrix number to 1 [BLOSUM 45], 2 [BLOSUM 62] or 3 [BLOSUM 80] (default 2) repeat-match Find all maximal exact matches in <genome-file> -E Use exhaustive (slow) search to find matches -f Forward strand only, don't use reverse complement -n # Set minimum exact match length to # -t Only output tandem repeats -V # Set 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 idenitity 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 consists of a list of coordinates, percent identity, and other useful information regarding the alignment data contained in the .delta file used as input. NOTE: No sorting is done by default, therefore the alignments will be ordered as found in the <deltafile> input. 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 consists of 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. This value specifies the distance from this SNP to the nearest mismatch (end of alignment, indel, SNP, etc) in the same alignment, while the [DIST] column specifies the distance from this SNP to the nearest sequence end. SNPs for which the [R] and [Q] columns are greater than 0 should be evaluated with caution, as these columns specify the number of other alignments which overlap this position. Use -C to assure SNPs are only reported from unique alignment regions. 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 consists of 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

//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. May 21, 2005 MUMMER(1)
 
 
 

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