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4 This manual is outdated, please refer to the HTML documentation included in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