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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 assembled contigs from metagenomes. Iff you want to identify CRISPRs in raw short read data, in the size range of 100-200bp try using Crass ( MinCED runs from the command-line and was derived from 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.


You need to install these dependencies first:

there is a Makefile in the source directory so installation should be as simple as:

cd <download_folder>

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!


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

You can also save both the table output and the gff output at the same time:

minced ecoli.fna out.txt out.gff


Copyright 2011      Florent ANGLY     <>
          2013-2019 Connor SKENNERTON <>

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
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 <>.


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