jpayne@69: -=- run-mummer3 (MUMmer3.0) README -=- jpayne@69: jpayne@69: ** NOTE ** jpayne@69: This manual is outdated, please refer to the HTML documentation included in jpayne@69: this distribution or at: jpayne@69: jpayne@69: http://mummer.sourceforge.net jpayne@69: http://mummer.sourceforge.net/manual jpayne@69: http://mummer.sourceforge.net/examples jpayne@69: jpayne@69: If any of this code is used in any publication, please cite the following: jpayne@69: jpayne@69: Fast algorithms for large-scale genome alignment and comparison. jpayne@69: A.L. Delcher. A. Phillippy, J. Carlton, and S.L. Salzberg. Nucleic jpayne@69: Acids Research 30:11 (2002), 2478-2483. jpayne@69: jpayne@69: jpayne@69: USAGE: ./run-mummer3 jpayne@69: jpayne@69: specifies the file with the first sequence in FastA jpayne@69: format. No more than on sequence is allowed. jpayne@69: specifies the multi-fasta sequence FastA file that contains jpayne@69: the query sequences, to be aligned to the reference. jpayne@69: specifies the file prefix for the output files. jpayne@69: jpayne@69: NOTE: jpayne@69: Coordinates from this script will be relative to their respective jpayne@69: strand. Thus reverse matches will have coordinates that reference the jpayne@69: reverse complemented query sequence! If this coordinate system is jpayne@69: confusing, use nucmer instead. jpayne@69: jpayne@69: jpayne@69: MATCHING PARAMETERS: jpayne@69: It is important to customize the command line parameters of the matching jpayne@69: and clustering algorithms to reflect the users desired alignment results. jpayne@69: All of the programs in the run-mummer3 script (mummer, mgaps, and combineMUMs) jpayne@69: can be passed various parameters to alter their performance and output. To view jpayne@69: these options, run each program from the command line with the "-h" option to jpayne@69: view their definable parameters. Then to make a permanent change to the script, jpayne@69: simply add the desired parameters to the script using a standard text editor. jpayne@69: jpayne@69: NOTE: For SNP hunters the -D option to combineMUMs will be very handy for jpayne@69: locating and parsing the difference positions. jpayne@69: jpayne@69: jpayne@69: MATCHING ALGORITHMS: jpayne@69: It is also possible to change the matching algorithm used in the alignment jpayne@69: generation. type 'mummer -help' to see the algorithm switches. jpayne@69: jpayne@69: jpayne@69: OUTPUT FILES: jpayne@69: The four output files of this script are: jpayne@69: .out jpayne@69: .gaps jpayne@69: .errorsgaps jpayne@69: .align jpayne@69: jpayne@69: + .out jpayne@69: This file lists the coordinates of the matches found and the length jpayne@69: of each match found. A group of matches to a specific sequence in jpayne@69: the query file is headed by the FastA tag of that sequence. The first jpayne@69: and second columns list the start coordinates in the reference and jpayne@69: query sequences respectively. The final column is the length of the jpayne@69: match. jpayne@69: jpayne@69: + .gaps jpayne@69: The headers and 1st - 3rd columns of this file are exactly like the jpayne@69: .out file above. However, matches are now sorted and clustered jpayne@69: according to their position in each of the sequences. Clusters of jpayne@69: matches are separated by a "#" character and matches from different jpayne@69: sequences in the query file are still separated by the FastA header jpayne@69: for that sequence. jpayne@69: The additional columns in this file (4th - 6th) describe jpayne@69: the gaps between adjacent matches. The 4th column represents the jpayne@69: number of overlapping characters between the current match and the jpayne@69: previous match. The 5th column displays the number of characters jpayne@69: between the beginning of this match in the reference and the end jpayne@69: of the previous match in the reference. Finally, the 6th column jpayne@69: displays the number of characters between the beginning of this jpayne@69: match in the query sequence and the end of the previous match in jpayne@69: the query sequence. jpayne@69: jpayne@69: + .errorsgaps jpayne@69: This file is identical to the .gaps file, except for the jpayne@69: addition of a 7th column that displays the number of errors in the jpayne@69: gap described by columns 5 and 6. This is perhaps the most helpful jpayne@69: output file of the script, as it is easy to parse and interpret. jpayne@69: jpayne@69: + .align jpayne@69: This file also expands on the .gaps file, but in a different jpayne@69: way than the witherrors.gaps file. This file intersperses the lines jpayne@69: of the .gaps file with an actual alignment of the gap between jpayne@69: the previous two matches. Additionally, wherever there was a "#" jpayne@69: character in the .gaps file, the .align file adds jpayne@69: a line that lists the encompassing start and stop coordinates of the jpayne@69: previous alignment region, a error ratio, and an error percentage. jpayne@69: jpayne@69: jpayne@69: Email questions, comments or bug reports to: