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78 changes: 40 additions & 38 deletions MANUAL.md
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Original file line number Diff line number Diff line change
@@ -1,11 +1,10 @@
# MUMmer4.x README

**NOTE**
**NOTES**

Further documentation, but potentially out of date, is in the [docs](../../tree/master/docs) directory. Please refer to the [INSTALL.md](INSTALL.md) file for installation
instructions.
Further, but potentially out of date, documentation can be found in the [docs](../../tree/master/docs) directory. Please refer to the [INSTALL.md](INSTALL.md) file for installation instructions.

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

Expand All @@ -16,11 +15,11 @@ 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
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
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
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:
Expand All @@ -44,9 +43,9 @@ system:

## RUNNING MUMmer4.x

MUMmer4.x is comprised of many various utilities
MUMmer4.x is composed of various utilities
and scripts. For general purposes, the programs `nucmer`, and
`promer` will be all that is needed. See their descriptions in the
`promer` are 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
Expand All @@ -56,17 +55,17 @@ utilities in this directory.

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:
format (qry.seq), type the following at the command line:

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

To produce the following files:

<prefix>.delta
`<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
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.

Expand Down Expand Up @@ -94,10 +93,13 @@ descriptions and usage definitions for these scripts. Please refer to the
`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"
cases are:

- Comparing two unfinished shotgun sequencing assemblies
- Mapping an unfinished sequencing assembly to a finished genome
- 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.

Expand All @@ -119,7 +121,7 @@ for more information regarding this script and its output, or type
**Notes:**

All output coordinates reference the forward strand of the involved
sequence, regardless of the match direction. Also, nucmer now uses
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.

Expand All @@ -131,14 +133,17 @@ use the '--mum' or '--maxmatch' options to change this behavior.
`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
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"
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
- 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.

Expand All @@ -162,18 +167,15 @@ for more information regarding this script and its output, or type
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
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
query sequence. Please use `nucmer` or `promer` if this coordinate
system is confusing.


Expand Down Expand Up @@ -255,8 +257,8 @@ only be used on the output of the `gaps` program.

**Notes:**

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


### combineMUMs
Expand Down Expand Up @@ -297,7 +299,7 @@ behavior and only outputs the positions of difference, e.g. SNPs.
**Description:**

This program filters a delta alignment file produced by either
nucmer or promer, leaving only the desired alignments which
`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
Expand Down Expand Up @@ -422,8 +424,8 @@ like the old `max-match` program.

`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
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:
Expand Down Expand Up @@ -459,7 +461,7 @@ postscript terminal and avoid the png terminal.

**Description:**

Script for plotting nucmer hits against a reference sequence. See top
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.

Expand Down Expand Up @@ -703,11 +705,11 @@ analysis.
**Description:**

This program reports polymorphism contained in a delta encoded
alignment file output by either nucmer or promer. It catalogs
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
alignments. Polymorphisms are reported one per line in a
delimited fashion similar to the output of `how-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.
Expand Down