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-=- run-mummer3 (MUMmer3.0) README -=-
** NOTE **
This manual is outdated, please refer to the HTML documentation included in
this distribution or at:
http://mummer.sourceforge.net
http://mummer.sourceforge.net/manual
http://mummer.sourceforge.net/examples
If any of this code is used in any publication, please cite the following:
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.
USAGE: ./run-mummer3 <reference> <query> <file prefix>
<reference> specifies the file with the first sequence in FastA
format. No more than on sequence is allowed.
<query> specifies the multi-fasta sequence FastA file that contains
the query sequences, to be aligned to the reference.
<file prefix> specifies the file prefix for the output files.
NOTE:
Coordinates from this script will be relative to their respective
strand. Thus reverse matches will have coordinates that reference the
reverse complemented query sequence! If this coordinate system is
confusing, use nucmer instead.
MATCHING PARAMETERS:
It is important to customize the command line parameters of the matching
and clustering algorithms to reflect the users desired alignment results.
All of the programs in the run-mummer3 script (mummer, mgaps, and combineMUMs)
can be passed various parameters to alter their performance and output. To view
these options, run each program from the command line with the "-h" option to
view their definable parameters. Then to make a permanent change to the script,
simply add the desired parameters to the script using a standard text editor.
NOTE: For SNP hunters the -D option to combineMUMs will be very handy for
locating and parsing the difference positions.
MATCHING ALGORITHMS:
It is also possible to change the matching algorithm used in the alignment
generation. type 'mummer -help' to see the algorithm switches.
OUTPUT FILES:
The four output files of this script are:
<prefix>.out
<prefix>.gaps
<prefix>.errorsgaps
<prefix>.align
+ <prefix>.out
This file lists the coordinates of the matches found and the length
of each match found. A group of matches to a specific sequence in
the query file is headed by the FastA tag of that sequence. The first
and second columns list the start coordinates in the reference and
query sequences respectively. The final column is the length of the
match.
+ <prefix>.gaps
The headers and 1st - 3rd columns of this file are exactly like the
<prefix>.out file above. However, matches are now sorted and clustered
according to their position in each of the sequences. Clusters of
matches are separated by a "#" character and matches from different
sequences in the query file are still separated by the FastA header
for that sequence.
The additional columns in this file (4th - 6th) describe
the gaps between adjacent matches. The 4th column represents the
number of overlapping characters between the current match and the
previous match. The 5th column displays the number of characters
between the beginning of this match in the reference and the end
of the previous match in the reference. Finally, the 6th column
displays the number of characters between the beginning of this
match in the query sequence and the end of the previous match in
the query sequence.
+ <prefix>.errorsgaps
This file is identical to the <prefix>.gaps file, except for the
addition of a 7th column that displays the number of errors in the
gap described by columns 5 and 6. This is perhaps the most helpful
output file of the script, as it is easy to parse and interpret.
+ <prefix>.align
This file also expands on the <prefix>.gaps file, but in a different
way than the witherrors.gaps file. This file intersperses the lines
of the <prefix>.gaps file with an actual alignment of the gap between
the previous two matches. Additionally, wherever there was a "#"
character in the <prefix>.gaps file, the <prefix>.align file adds
a line that lists the encompassing start and stop coordinates of the
previous alignment region, a error ratio, and an error percentage.
Email questions, comments or bug reports to: <mummer-help@lists.sourceforge.net>
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