Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/docs/run-mummer3.README @ 69:33d812a61356

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
parents
children
comparison
equal deleted inserted replaced
67:0e9998148a16 69:33d812a61356
1 -=- run-mummer3 (MUMmer3.0) README -=-
2
3 ** NOTE **
4 This manual is outdated, please refer to the HTML documentation included in
5 this distribution or at:
6
7 http://mummer.sourceforge.net
8 http://mummer.sourceforge.net/manual
9 http://mummer.sourceforge.net/examples
10
11 If any of this code is used in any publication, please cite the following:
12
13 Fast algorithms for large-scale genome alignment and comparison.
14 A.L. Delcher. A. Phillippy, J. Carlton, and S.L. Salzberg. Nucleic
15 Acids Research 30:11 (2002), 2478-2483.
16
17
18 USAGE: ./run-mummer3 <reference> <query> <file prefix>
19
20 <reference> specifies the file with the first sequence in FastA
21 format. No more than on sequence is allowed.
22 <query> specifies the multi-fasta sequence FastA file that contains
23 the query sequences, to be aligned to the reference.
24 <file prefix> specifies the file prefix for the output files.
25
26 NOTE:
27 Coordinates from this script will be relative to their respective
28 strand. Thus reverse matches will have coordinates that reference the
29 reverse complemented query sequence! If this coordinate system is
30 confusing, use nucmer instead.
31
32
33 MATCHING PARAMETERS:
34 It is important to customize the command line parameters of the matching
35 and clustering algorithms to reflect the users desired alignment results.
36 All of the programs in the run-mummer3 script (mummer, mgaps, and combineMUMs)
37 can be passed various parameters to alter their performance and output. To view
38 these options, run each program from the command line with the "-h" option to
39 view their definable parameters. Then to make a permanent change to the script,
40 simply add the desired parameters to the script using a standard text editor.
41
42 NOTE: For SNP hunters the -D option to combineMUMs will be very handy for
43 locating and parsing the difference positions.
44
45
46 MATCHING ALGORITHMS:
47 It is also possible to change the matching algorithm used in the alignment
48 generation. type 'mummer -help' to see the algorithm switches.
49
50
51 OUTPUT FILES:
52 The four output files of this script are:
53 <prefix>.out
54 <prefix>.gaps
55 <prefix>.errorsgaps
56 <prefix>.align
57
58 + <prefix>.out
59 This file lists the coordinates of the matches found and the length
60 of each match found. A group of matches to a specific sequence in
61 the query file is headed by the FastA tag of that sequence. The first
62 and second columns list the start coordinates in the reference and
63 query sequences respectively. The final column is the length of the
64 match.
65
66 + <prefix>.gaps
67 The headers and 1st - 3rd columns of this file are exactly like the
68 <prefix>.out file above. However, matches are now sorted and clustered
69 according to their position in each of the sequences. Clusters of
70 matches are separated by a "#" character and matches from different
71 sequences in the query file are still separated by the FastA header
72 for that sequence.
73 The additional columns in this file (4th - 6th) describe
74 the gaps between adjacent matches. The 4th column represents the
75 number of overlapping characters between the current match and the
76 previous match. The 5th column displays the number of characters
77 between the beginning of this match in the reference and the end
78 of the previous match in the reference. Finally, the 6th column
79 displays the number of characters between the beginning of this
80 match in the query sequence and the end of the previous match in
81 the query sequence.
82
83 + <prefix>.errorsgaps
84 This file is identical to the <prefix>.gaps file, except for the
85 addition of a 7th column that displays the number of errors in the
86 gap described by columns 5 and 6. This is perhaps the most helpful
87 output file of the script, as it is easy to parse and interpret.
88
89 + <prefix>.align
90 This file also expands on the <prefix>.gaps file, but in a different
91 way than the witherrors.gaps file. This file intersperses the lines
92 of the <prefix>.gaps file with an actual alignment of the gap between
93 the previous two matches. Additionally, wherever there was a "#"
94 character in the <prefix>.gaps file, the <prefix>.align file adds
95 a line that lists the encompassing start and stop coordinates of the
96 previous alignment region, a error ratio, and an error percentage.
97
98
99 Email questions, comments or bug reports to: <mummer-help@lists.sourceforge.net>