rstatstartu/minced repository overview

docker run rstatstartu/minced

MinCED, a program to find CRISPRs in shotgun DNA sequences or full genomes                              

Usage:    minced [options] file.fa [outputFile.txt] [outputFile.gff]

Options:  -searchWL  Length of search window used to discover CRISPRs (range: 6-9). Default: 8
          -minNR     Minimum number of repeats a CRISPR must contain. Default: 3
          -minRL     Minimum length of the CRISPR repeats. Default: 23
          -maxRL     Maximum length of the CRISPR repeats. Default: 47
          -minSL     Minimum length of the CRISPR spacers. Default: 26
          -maxSL     Maximum length of the CRISPR spacers. Default: 50
          -gff       Output summary results in gff format containing
                     only the positions of the CRISPR arrays. Default: false
          -gffFull   Output detailed results in gff format containing
                     positions of CRISPR arrays and all repeat units. Default: false
          -spacers   Output a fasta formatted file containing the spacers. Default: false
          -h --help  Output this handy help message
          --version  Output version information

Examples: minced ecoli.fna
          minced metagenome.fna
          minced metagenome.fna metagenome.crisprs
          minced metagenome.fna metagenome.crisprs metagenome.gff

docker run rstatstartu/minced t/Aquifex_aeolicus_VF5.fna

Sequence 'gi|15282445|ref|NC_000918.1|' (1551335 bp)

CRISPR 1   Range: 156460 - 156767
POSITION        REPEAT                          SPACER
--------        ------------------------------  ---------------------------------------
156460          GTTCCTAATGTACCGTGTGGAGTTGAAACC  CAGTCAGATTGAAGTTATCGTCAACTTCAAAATACG    [ 30, 36 ]
156526          GTTCCTAATGTACCGTGTGGAGTTGAAACC  TTGCTTTATCAGAGAATAGTATTCTTTCTATGTCTTCATAGTTT       [ 30, 44 ]
156600          GTTCCTAATGTACCGTGTGGAGTTGAAACC  TCTTGATAGTATCTGTTTTCCGCGTATTCCACGATTCTTTT [ 30, 41 ]
156671          GTTCCTAATGTACCGTAGTGGAGTTGAAAC  TTCGGTGATAAAGGAGCATTTTTCACAAAAGAAATCA   [ 30, 37 ]
156738          GTTTCTAATGTACCGTGTGGATAAAAATGA
--------        ------------------------------  ---------------------------------------
Repeats: 5      Average Length: 30              Average Length: 39

CRISPR 2   Range: 244561 - 244791
POSITION        REPEAT                          SPACER
--------        -----------------------------   --------------------------------------
244561          GTTTCAACTCCACACGGTACATTAGGAAC   ATGACATTTCAGGAGGTGGAGCATGATTACTATCTTTTC [ 29, 39 ]
244629          GTTTCAACTCCACACGGTACATTAGGAAC   AGTATAAGCTTTCTAAGCCTTGAAAGGAAAAGCTCCTCGC  [ 29, 40 ]
244698          GTTTCAACTCCACACGGTACATTAGGAAC   TCTCTACCTTCCTTTCAACCTGTATTGCTATGTCCG    [ 29, 36 ]
244763          GTTTCAACTCCACACGGTACATTAGGAAC
--------        -----------------------------   --------------------------------------
Repeats: 4      Average Length: 29              Average Length: 38

CRISPR 3   Range: 279264 - 279555
POSITION        REPEAT                          SPACER
--------        -----------------------------   ------------------------------------
279264          GTTTTAACTCCACACGGTACATTAGAAAC   CATCTGCAACATATTCAAGTTCAGCTTCAAAACCTT    [ 29, 36 ]
279329          GTTTTAACTCCACACGGTACATTAGAAAC   TTCGTCAAGCTTTACCTCAAAAGTCCTCTCAAACCT    [ 29, 36 ]
279394          GTTTTAACTCCACACGGTACATTAGAAAC   AATAATCAACAACTCTTTGATTTTGTGAAATGGAAGAA  [ 29, 38 ]
279461          GTTTTAACTCCACACGGTACATTAGAAAC   AGAACTCTCAGAAGAACCGAGAGCTTTTTCTATTAAC   [ 29, 37 ]
279527          GTTTTAACTCCACACGGTACATTAGAAAC
--------        -----------------------------   ------------------------------------
Repeats: 5      Average Length: 29              Average Length: 36

CRISPR 4   Range: 1226626 - 1226861
POSITION        REPEAT                          SPACER
--------        ------------------------------- -------------------------------------
1226626         GGTTTCTAATGTACCGTAGAGGAGTTGAAAC CAGAACAATAAGAGAGCCGATTGATGAGAACGCAGA    [ 31, 36 ]
1226693         CGTTTCTAATGTACCGTAGAGGAGTTGAAAC AGATATGATACACCTGAAACATTCTTTTACATGGAC    [ 31, 36 ]
1226760         CGTTTCTAATGTACCGTAGAGGAGTTGAAAC CCGGCGGATATAAAAATCGCCTACCTATACGCCGTAATGG  [ 31, 40 ]
1226831         CGTTTCTAATGTACCGTGTGGAGTTAAAACA
--------        ------------------------------- -------------------------------------
Repeats: 4      Average Length: 31              Average Length: 37

CRISPR 5   Range: 1379598 - 1379894
POSITION        REPEAT                          SPACER
--------        ------------------------------  ------------------------------------
1379598         ATAGCTTCTTCCACACGGTACATTAGGAAC  AAAGAAAATCCAAGAAATGTCCACGCCCTCCGAAGTCA  [ 30, 38 ]
1379666         GTTTCAACTCCACTACGGTACATTAGGAAC  TTATTTAGCATTCAAAAAAGGAGTTCTTGTAAATACA   [ 30, 37 ]
1379733         GTTTCAACTCCACTACGGTACATTAGGAAC  AAGTGAGGAGATGGGAAAGACATGAGGAAATTCTAC    [ 30, 36 ]
1379799         GTTTCAACTCCACTACGGTACATTAGGAAC  TGCTGGATTTCCCTTCCTTATTTTAATGTTCATTAC    [ 30, 36 ]
1379865         GTTTCAACTCCACTACGGTACATTAGGAAC
--------        ------------------------------  ------------------------------------
Repeats: 5      Average Length: 30              Average Length: 36

CRISPR 6   Range: 1418900 - 1419060
POSITION        REPEAT                          SPACER
--------        -----------------------------   -------------------------------------
1418900         GTTCCTAATGTACCGTGTGGAGTTGAAAC   CATAATAGGAGAATTTAGGAATGCTGATATGCGGGA    [ 29, 36 ]
1418965         GTTCCTAATGTACCGTGTGGAGTTGAAAC   TTGTCGAGAATTACATCGTCAGGAGTTTCTACTTCAAG  [ 29, 38 ]
1419032         GTTCCTAATGTACCGTGTGGAGTTGAAAC
--------        -----------------------------   -------------------------------------
Repeats: 3      Average Length: 29              Average Length: 37

Time to find repeats: 371 ms