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| MinCED - Mining CRISPRs in Environmental Datasets | |
| MinCED is a program to find Clustered Regularly Interspaced Short Palindromic | |
| Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes, | |
| in which sequence size can be anywhere from 100 to 800 bp. MinCED runs from the | |
| command-line and was derived from CRT (http://www.room220.com/crt/): | |
| Charles Bland et al., CRISPR Recognition Tool (CRT): a tool for automatic | |
| detection of clustered regularly interspaced palindromic repeats, BMC | |
| Bioinformatics 8, no. 1 (2007): 209. | |
| INSTALLATION | |
| You need to install these dependencies first: | |
| * Java (http://www.java.com/en/download/) | |
| there is a Makefile in the source directory so installation should be as simple as: | |
| $ cd <download_folder> | |
| $ make | |
| To run MinCED: | |
| $ ./minced [options] file.fa | |
| The help page can be obtained by typing: | |
| $ ./minced --help | |
| You can get the MinCED version this way: | |
| $ ./minced --version | |
| NOTE: Always keep `minced` and `minced.jar` in the same folder! | |
| EXAMPLES | |
| Finding CRISPRs in the E. coli genome: | |
| $ minced ecoli.fna | |
| To find repeats in short sequences, we need to decrease the minimum number of | |
| repeats to find. For example, in 100 bp reads, we could not possibly find more | |
| than 2 repeats: | |
| $ minced -minNR 2 metagenome.fna | |
| The output can be large, so save it in a file: | |
| $ minced -minNR 2 metagenome.fna metagenome.crisprs | |
| COPYRIGHT AND LICENSE | |
| Copyright 2011 Florent ANGLY <florent.angly@gmail.com> | |
| 2013-2015 Connor SKENNERTON <c.skennerton@gmail.com> | |
| MinCED is free software: you can redistribute it and/or modify | |
| it under the terms of the GNU General Public License as published by | |
| the Free Software Foundation, either version 3 of the License, or | |
| (at your option) any later version. | |
| MinCED is distributed in the hope that it will be useful, | |
| but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| GNU General Public License for more details. | |
| You should have received a copy of the GNU General Public License | |
| along with MinCED. If not, see <http://www.gnu.org/licenses/>. | |
| BUGS | |
| All complex software has bugs lurking in it, and this program is no exception. | |
| If you find a bug please post an issue on github https://github.com/ctSkennerton/minced/issues |