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MUMmer4.x README

NOTE

Further documentation, but potentially out of date, is in the docs directory. Please refer to the INSTALL.md file for installation instructions.

This file contains brief descriptions of all executables in the base directory and general information about the MUMmer package.

DESCRIPTION

MUMmer is a system for rapidly aligning entire genomes. The current version (release 4.x) can find all 20 base pair maximal exact matches between two bacterial genomes of ~5 million base pairs each in 20 seconds, using 90 MB of memory, on a typical 1.8 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome, using the nucmer utility included with the system. The promer utility takes this a step further by generating alignments based upon the six-frame translations of both input sequences. promer permits the alignment of genomes for which the proteins are similar but the DNA sequence is too divergent to detect similarity. See the nucmer and promer readme files in the "docs/" subdirectory for more details. MUMmer is open source, so all we ask is that you cite our most recent paper in any publications that use this system:

(Version 3.0 described)

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.

(Version 2.1 described)

Fast algorithms for large-scale genome alignment and comparison.
A.L. Delcher. A. Phillippy, J. Carlton, and S.L. Salzberg.
Nucleic Acids Research 30:11 (2002), 2478-2483.

(Version 1.0 described)

Alignment of Whole Genomes.
A.L. Delcher, S. Kasif,R.D. Fleischmann, J. Peterson, O. White, and S.L. Salzberg.
Nucleic Acids Research, 27:11 (1999), 2369-2376.

RUNNING MUMmer4.x

MUMmer4.x is comprised of many various utilities and scripts. For general purposes, the programs nucmer, and promer will be all that is needed. See their descriptions in the "RUNNING THE MUMmer PROGRAMS" section, or refer to their individual documentation in the "docs/" subdirectory. Refer to the "RUNNING THE MUMmer UTILITIES" section for a brief description of all of the utilities in this directory.

Simple use case

Given a file containing a single reference sequence (ref.seq) in FASTA format and another file containing multiple sequences in FastA format (qry.seq) type the following at the command line:

./nucmer -p <prefix> ref.seq qry.seq

To produce the following files:

<prefix>.delta

Please read the utility-specific documentation in the "docs/" subdirectory for descriptions of these files and information on how to change the alignment parameters for the scripts (minimum match length, etc.), or see the notes below in the "RUNNING THE MUMmer SCRIPTS" section for a brief explanation.

To see a simple gnuplot output, if you have gnuplot installed, run the perl script mummerplot on the output files. This script can be run on mummer output (.out), or nucmer/promer output (.delta). Edit the .gp file that is created to change colors, line thicknesses, etc. or explore the <prefix>.[fr]plot file to see the data collection.

./mummerplot -p <prefix> <prefix>.out

RUNNING THE MUMmer SCRIPTS

Because of MUMmer's modular design, it may be necessary to use a number of separate programs to produce the desired output. The MUMmer scripts attempt to simplify this process by wrapping various utilities into packages that can perform standard alignment requests. Listed below are brief descriptions and usage definitions for these scripts. Please refer to the "docs/" subdirectory for a more detailed description of each script.

nucmer

Description:

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. Please refer to "docs/nucmer.README" for more information regarding this script and its output, or type nucmer -h for a list of its options.

    USAGE:
    nucmer  [options]  <reference>  <query>

    [options]    type 'nucmer -h' for a list of options.
    <reference>  specifies the multi-FastA sequence file that contains
                 the reference sequences, to be aligned with the queries.
    <query>      specifies the multi-FastA sequence file that contains
                 the query sequences, to be aligned with the references.

    OUTPUT:
    out.delta    the delta encoded alignments between the reference and
                 query sequences.  This file can be parsed with any of
                 the show-* programs which are described in the "RUNNING
                 THE MUMmer UTILITIES" section.

Notes:

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 the '--mum' or '--maxmatch' options to change this behavior.

promer

Description:

promer is for the protein level, all-vs-all comparison of nucleotide sequences contained in multi-FastA data files. The nucleotide input files are translated in all 6 reading frames and then aligned to one another via the same methods as nucmer. It is best used for highly divergent sequences that may have moderate to high similarity on the protein level. Common use cases are: identifying syntenic regions between highly divergent genomes, comparative genome annotation i.e. using an already annotated genome to help in the annotation of a newly sequenced genome, and the general comparison of two fairly divergent genomes that have large rearrangements and may only be similar on the protein level. Please refer to "docs/promer.README" for more information regarding this script and its output, or type promer -h for a list of its options.

    USAGE:
    promer  [options]  <reference>  <query>

    [options]    type 'promer -h' for a list of options.
    <reference>  specifies the multi-FastA sequence file that contains
                 the reference sequences, to be aligned with the queries.
    <query>      specifies the multi-FastA sequence file that contains
                 the query sequences, to be aligned with the references.

    OUTPUT:
    out.delta    the delta encoded alignments between the reference and
                 query sequences.  This file can be parsed with any of
                 the show-* programs which are described in the "RUNNING
                 THE MUMmer UTILITIES" section.

Notes:

All output coordinates reference the forward strand of the involved sequence, regardless of the match direction, and are measured in nucleotides with the exception of the delta integers which are measured in amino acids (1 delta int = 3 nucleotides). Also, promer now uses only matches that are unique in the reference sequence by default, use the '--mum' or '--maxmatch' options to change this behavior.

Notes:

All output coordinates reference their respective strand. This means that for all reverse matches, the coordinates that reference the query sequence will be relative to the reverse complement of the query sequence. Please use nucmer or promer if this coordinate system is confusing.

dnadiff

Description:

This script is a wrapper around nucmer that builds an alignment using default parameters, and runs many of nucmer's helper scripts to process the output and report alignment statistics, SNPs, breakpoints, etc. It is designed for evaluating the sequence and structural similarity of two highly similar sequence sets. E.g. comparing two different assemblies of the same organism, or comparing two strains of the same species. Please refer to "docs/dnadiff.README" for more information regarding this script and its output, or type 'dnadiff -h' for a list of its options.

    USAGE: dnadiff  [options]  <reference>  <query>
      or   dnadiff  [options]  -d <delta file>

    <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

    OUTPUT:
    .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)

Notes:

The report file generated by this script can be useful for comparing the differences between two similar genomes or assemblies. The other outputs generated by this script are in unlabeled tabular format, so please refer to the utility specific documentation for interpreting them. A full description of the report file is given in "docs/dnadiff.README".

RUNNING THE MUMmer UTILITIES

The MUMmer package consists of various utilities that can interact with the mummer program. mummer performs all maximal and maximal unique matching, and all other utilities were designed to process the input and output of this program and its related scripts, in order to extract additional information from the output. Listed below are the descriptions and usage definitions for these utilities.

annotate

Description: This program reads the output of the gaps program and adds alignment information to it. Part of the original MUMmer1.0 pipeline and can only be used on the output of the gaps program.

    USAGE:
    annotate  <gapsfile>  <seq2>

    <gapsfile>  the output of the 'gaps' program.
    <seq2>      the file containing the second sequence in the comparison.

    OUTPUT:
    stdout           the 'gaps' output interspersed with the alignments of
                     the gaps between adjacent MUMs.  An alignment of a
                     gap comes after the second MUM defining the gap, and
                     alignment errors are marked with a '^' character.
    witherrors.gaps  the 'gaps' output with an appended column that lists
                     the number of alignment errors for each gap.

Notes:

This program will eventually be dropped in favor of the combineMUMs or nucmer match extenders, but persists for the time being.

combineMUMs

Description:

This program reads the output of the mgaps program and adds alignment information to it. Part of the MUMmer4.x pipeline and can only be used on the output of the mgaps program. This -D option alters this behavior and only outputs the positions of difference, e.g. SNPs.

    USAGE:
    combineMUMs  [options]  <reference>  <query>  <mgapsfile>

    [options]    type 'combineMUMs -h' for a list of options.
    <reference>  the FastA reference file used in the comparison.
    <query>      the multi-FastA reference file used in the comparison.
    <mgapsfile>  the output of the 'mgaps' program run on the match
                 list produced by 'mummer' for the reference and query
                 files.

    OUTPUT:
    stdout           the 'mgaps' output interspersed with the alignments
                     of the gaps between adjacent MUMs.  An alignment of a
                     gap comes after the second MUM defining the gap, and
                     alignment errors are marked with a '^' character.  At
                     the end of each cluster is a summary line (keyword
                     "Region") noting the bounds of the cluster in the
                     reference and query sequences, the total number of
                     errors for the region, the length of the region and
                     the percent error of the region.
    witherrors.gaps  the 'mgaps' output with an appended column that lists
                     the number of alignment errors for each gap.

delta-filter

Description:

This program filters a delta alignment file produced by either nucmer or promer, leaving only the desired alignments which are output to stdout in the same delta format as the input. Its primary function is the LIS algorithm which calculates the longest increasing subset of alignments. This allows for the calculation of a global set of alignments (i.e. 1-to-1 and mutually consistent order) with the -g option or locally consistent with -1 or -m. Reference sequences can be mapped to query sequences with -r, or queries to references with -q. This allows the user to exclude chance and repeat induced alignments, leaving only the "best" alignments between the two data sets. Filtering can also be performed on length, identity, and uniquenes.

    USAGE:
    delta-filter  [options]  <deltafile>

    [options]    type 'delta-filter -h' for a list of options.
    <deltafile>  the .delta output file from either nucmer or promer.

    OUTPUT:
    stdout  The same delta alignment format as output by nucmer and promer.

Notes:

For most cases the -m option is recommended, however -1 is useful for applications that require a 1-to-1 mapping, such as SNP finding. Use the -q option for mapping query contigs to their best reference location.

exact-tandems

Description:

This script finds exact tandem repeats in a specified FastA sequence file. It is a post-processor for repeat-match and provides a simple interface and output for tandem repeat detection.

    USAGE:
    exact-tandems  <file>  <min match>

    <file>       the single sequence in FastA format to search for repeats.
    <min match>  the minimum match length for the tandems.

    OUTPUT:
    stdout  4 columns, the start of the tandem repeat, the total extent
            of the repeat region, the length of each repetitive unit, and
            to total copies of the repetitive unit involved.

mgaps

Description:

This program reads a list of matches between a single-FastA reference and a multi-FastA query file and outputs clusters of matches that lie on similar diagonals and within a reasonable distance. Part of the MUMmer4.x pipeline and the output of mummer need not be processed before passing it to this program, so long as mummer was run on a 1-vs-many or 1-vs-1 dataset.

    USAGE:
    mgaps  [options]  <  <matchlist>

    [options]    type 'mgaps -h' for a list of options.
    <matchlist>  A list of matches separated by their sequence FastA tags.
                 The columns of the match list should be start in
                 reference, start in query, and length of the match.

    OUTPUT:
    stdout  An ordered set of the input matches, separated by headers.
            Individual clusters are separated by a '#' character and
            sets of clusters from different sequences are separated by
            the FastA header tag for the query sequence.

Notes:

It is often very helpful to adjust the clustering parameters. Check mgaps -h for the list of parameters and check the source for a better idea of how each parameter affects the result. Often, it is helpful to run this program a number of times with different parameters until the desired result is achieved.

mummer

Description:

This is the core program of the MUMmer package. It is the suffix-tree based match finding routine, and the main part of every MUMmer script. For a detailed manual describing how to use this program, please refer to "docs/maxmat3man.pdf" or in LaTeX format "docs/maxmat3man.tex". By default, mummer now finds maximal matches regardless of their uniqueness. Limiting the output to only unique matches can be specified as a command line switch.

    USAGE:
    mummer  [options]  <reference>  <query> ...

    [options]    type 'mummer -help' for a list of options.
    <reference>  specifies the single or multi-FastA sequence file that
                 contains the reference sequence(s), to be aligned with
                 the queries.
    <query>      specifies the multi-FastA sequence file that contains
                 the query sequences, to be aligned with the references.
                 Multiple query files are allowed, up to 32.

    OUTPUT:
    stdout  a list of exact matches. Varies depending on input, refer to
            the manual specified in the description above.

Notes:

Many thanks to Stefan Kurtz for the latest mummer version. mummer now behaves like the old mummer2 program by default. The -mum switch forces it to behave like mummer1, the -mumreference switch forces it to behave like mummer2 while the -maxmatch switch forces it to behave like the old max-match program.

mummerplot

Description:

mummerplot is a perl script that generates gnuplot scripts and data collections for plotting with the gnuplot utility. It can generate 2-d dotplots and 1-d coverage plots for the output of mummer, nucmer, promer or show-tiling. It can also color dotplots with an identity color gradient.

    USAGE:
    mummerplot  [options]  <matchfile>

    [options]    type 'mummerplot -h' for a list of options.
    <matchfile>  the output of 'mummer', 'nucmer', 'promer', or
                 'show-tiling'. 'mummerplot' will automatically determine
                 the format of the data it was given and produce the plot
                 accordingly.

    OUTPUT:
    out.gp     The gnuplot script, type 'gnuplot out.gp' to evaluate the
               the gnuplot script.
    out.fplot
    out.rplot
    out.hplot  The forward, reverse and highlighted match information for
               plotting with gnuplot.

    out.ps
    out.png    The plotted image file, postscript or png depending on the
               selected terminal type.

Notes:

For alignments with multiple reference or query sequences, be sure to use the -r -q or -R -Q options to avoid overlaying multiple plots in the same space. For better looking color gradient plots, try the postscript terminal and avoid the png terminal.

nucmer2xfig

Description:

Script for plotting nucmer hits against a reference sequence. See top of script for more information, or see if mummerplot or mapview has the functionality required as they are properly maintained.

repeat-match

Description:

Finds exact repeats within a single sequence.

    USAGE:
    repeat-match  [options]  <seq>

    [options]  type 'repeat-match -h' for a list of options.
    <seq>      the single sequence in FastA format to search for repeats.

    OUTPUT:
    stdout  3 columns, the start of the first copy of the repeat, the
            start of the second copy of the repeat, and the length of the
            repeat respectively.

Notes:

REPuter (freely available for universities) may be better suited for most repeat matching, but repeat-match is open-source and has some functionality that REPuter does not so we include it along with the MUMmer package.

show-aligns

Description:

This program parses the delta alignment output of nucmer and promer and displays all of the pairwise alignments from the two sequences specified on the command line.

    USAGE:
    show-aligns  [options]  <deltafile>  <IdR>  <IdQ>

    [options]    type 'show-aligns -h' for a list of options.
    <deltafile>  the .delta output file from either nucmer or promer.
    <IdR>        the FastA header tag of the desired reference sequence.
    <IdQ>        the FastA header tag of the desired query sequence.

    OUTPUT:
    stdout  each alignment header and footer describes the frame of the
            alignment in each sequence, and the start and finish
            (inclusive) of the alignment in each sequence.  At the
            beginning of each line of aligned sequence are two numbers, the
            top is the coordinate of the first reference base on that line
            and the bottom is the coordinate of the first query base on
            that line.  ALL coordinates reference the forward strand of the
            DNA sequence, even if it is a protein alignment.  A gap caused
            by an insertion or deletion is filled with a '.' character.
            Errors in a DNA alignment are marked with a '^' below the
            error.  Errors in an amino acid alignment are marked with a
            whitespace in the middle consensus line, while matches are
            marked with the consensus base and similarities are marked with
            a '+' in the consensus line.

show-coords

Description:

This program parses the delta alignment output of nucmer and promer and displays the coordinates, and other useful information about the alignments.

    USAGE:
    show-coords  [options]  <deltafile>

    [options]    type 'show-coords -h' for a list of options.
    <deltafile>  the .delta output file from either nucmer or promer.

    OUTPUT:
    stdout  run 'show-coords' without the -H option to see the column
            header tags.  Here is a description of each tag.  Note that
            some of the below tags do not apply to nucmer data, and that
            all coordinates are inclusive and relative to the forward DNA
            strand.

    [S1]    Start of the alignment region in the reference sequence.

    [E1]    End of the alignment region in the reference sequence.

    [S2]    Start of the alignment region in the query sequence.

    [E2]    End of the alignment region in the query sequence.

    [LEN 1] Length of the alignment region in the reference sequence,
    measured in nucleotides.

    [LEN 2] Length of the alignment region in the query sequence, measured
    in nucleotides.

    [% IDY] Percent identity of the alignment, calculated as the
    (number of exact matches) / ([LEN 1] + insertions in the query).

    [% SIM] Percent similarity of the alignment, calculated like the above
    value, but counting positive BLOSUM matrix scores instead of exact
    matches.

    [% STP] Percent of stop codons of the alignment, calculated as
    (number of stop codons) / (([LEN 1] + insertions in the query) * 2).

    [LEN R] Length of the reference sequence.

    [LEN Q] Length of the query sequence.

    [COV R] Percent coverage of the alignment on the reference sequence,
    calculated as [LEN 1] / [LEN R].

    [COV Q] Percent coverage of the alignment on the query sequence,
    calculated as [LEN 2] / [LEN Q].

    [FRM]   Reading frame for the reference sequence and the reading frame
    for the query sequence respectively.  This is one of the columns
    absent from the nucmer data, however, match direction can easily be
    determined by the start and end coordinates.

    [TAGS]  The reference FastA ID and the query FastA ID.

            There is also an optional final column (turned on with the -w
    or -o option) that will contain some 'annotations'. The -o option will
    annotate alignments that represent overlaps between two sequences,
    while the -w option is antiquated and should no longer be used.
    Sometimes, nucmer or promer will extend adjacent clusters past one
    another, thus causing a somewhat redundant output, this option will
    notify users of such rare occurrences.

Notes:

The -c and -l options are useful when comparing two sets of assembly contigs, in that these options help determine if an alignment spans an entire contig, or is just a partial hit to a different read. The -b option is useful when the user wishes to identify sytenic regions between two genomes, but is not particularly interested in the actual alignment similarity or appearance. This option also disregards match orientation, so should not be used if this information is needed.

show-diff

Description:

This program classifies alignment breakpoints for the quantification of macroscopic differences between two genomes. It takes a standard, unfiltered delta file as input, determines the best mapping between the two sequence sets, and reports on the breaks in that mapping.

    USAGE:
    show-diff  [options]  <deltafile>

    [options]    type 'show-diff -h' for a list of options.
    <deltafile>  the .delta output file from nucmer

    OUTPUT:
    stdout  Classified breakpoints are output one per line with
            the following types and column definitions. The first
            five columns of every row are seq ID, feature type,
            feature start, feature end, and feature length.

    Feature Columns

    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

    Feature Types

    [GAP] A gap between two mutually consistent ordered and
    oriented alignments. gap-length-R is the length of the
    alignment gap in the reference, gap-length-Q is the length of
    the alignment gap in the query, and gap-diff is the difference
    between the two gap lengths. If gap-diff is positive, sequence
    has been inserted in the reference. If gap-diff is negative,
    sequence has been deleted from the reference. If both
    gap-length-R and gap-length-Q are negative, the indel is
    tandem duplication copy difference.

    [DUP] A duplicated sequence in the reference that occurs more
    times in the reference than in the query. The coordinate
    columns specify the bounds and length of the
    duplication. These features are often bookended by BRK
    features if there is unique sequence bounding the duplication.

    [BRK] An insertion in the reference of unknown origin, that
    indicates no query sequence aligns to the sequence bounded by
    gap-start and gap-end. Often found around DUP elements or at
    the beginning or end of sequences.

    [JMP] A relocation event, where the consistent ordering of
    alignments is disrupted. The coordinate columns specify the
    breakpoints of the relocation in the reference, and the
    gap-length between them. A negative gap-length indicates the
    relocation occurred around a repetitive sequence, and a
    positive length indicates unique sequence between the
    alignments.

    [INV] The same as a relocation event, however both the
    ordering and orientation of the alignments is disrupted. Note
    that for JMP and INV, generally two features will be output,
    one for the beginning of the inverted region, and another for
    the end of the inverted region.

    [SEQ] A translocation event that requires jumping to a new
    query sequence in order to continue aligning to the
    reference. If each input sequence is a chromosome, these
    features correspond to inter-chromosomal translocations.

Notes:

The estimated number of features, take inversions for example, represents the number of breakpoints classified as bordering an inversion. Therefore, since there will be a breakpoint at both the beginning and the end of an inversion, the feature counts are roughly double the number of inversion events. In addition, all counts are estimates and do not represent the exact number of each evolutionary event.

Summing the fifth column (ignoring negative values) yeilds an estimate of the total inserted sequence in the reference. Summing the fifth column after removing DUP features yields an estimate of the total amount of unique (unaligned) sequence in the reference. Note that unaligned sequences are not counted, and could represent additional "unique" sequences. Use the dnadiff script if you must recover this information. Finally, the -q option switches references for queries, and uses the query coordinates for the analysis.

show-snps

Description:

This program reports polymorphism contained in a delta encoded alignment file output by either 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.

    USAGE:
    show-snps  [options]  <deltafile>

    [options]    type 'show-snps -h' for a list of options.
    <deltafile>  the .delta output file from either nucmer or promer.

    OUTPUT:
    stdout  Standard output has column headers with the following
            meanings. Not all columns will be output by default,
            see 'show-snps -h' for switch to control the output.

    [P1]    SNP position in the reference.

    [SUB]   Character in the reference.

    [SUB]   Character in the query.

    [P2]    SNP position in the query.

    [BUFF]  Distance from this SNP to the nearest mismatch (end of
    alignment, indel, SNP, etc) in the same alignment.

    [DIST]  Distance from this SNP to the nearest sequence end.

    [R]     Number of repeat alignments which cover this reference
    position, >0 means repetitive sequence.

    [Q]     Number of repeat alignments which cover this query
    position, >0 means repetitive sequence.

    [LEN R] Length of the reference sequence.

    [LEN Q] Length of the query sequence.

    [CTX R] Surrounding context sequence in the reference.

    [CTX Q] Surrounding context sequence in the query.

    [FRM]   Reading frame for the reference sequence and the
    reading frame for the query sequence respectively. Simply
    'forward' 1, or 'reverse' -1 for nucmer data.

    [TAGS]  The reference FastA ID and the query FastA ID.

Notes:

It is often helpful to run this with the -C option to assure reported SNPs are only reported from uniquely aligned regions.

show-tiling

Description:

This program 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 location on a reference for each 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 the the references.

    USAGE:
    show-tiling  [options]  <deltafile>

    [options]    type 'show-tiling -h' for a list of options.
    <deltafile>  the .delta output file from either nucmer or promer.

    OUTPUT:
    stdout  Standard output has 8 columns: start in reference, end in
            reference, gap between this contig and the next, length of this
            contig, alignment coverage of this contig, average percent
            identity of the alignments for this contig, orientation of this
            contig, contig ID. All matches to a reference are headed by the
            FASTA tag of that reference.  Output with the -a option is the
            same as 'show-coords -cl' when run on nucmer data.

Notes:

When run with the -x option, show-tiling will produce an XML output format that can be accepted by TIGR's open source scaffolding software 'Bambus' as contig linking information.

Obsolete programs

The programs mapview, run-mummer1, run-mummer3 and nucmer2xfig are now obsolete. The original documentation is still available in OBSOLETE.md.

CONTACT INFORMATION

Please address questions and bug reports via the github issue tracker.