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Close assembly gaps using long-reads with focus on correctness.
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README.md

dentist

Close assembly gaps using long-reads with focus on correctness.

Building

git clone https://github.com/a-ludi/dentist.git
cd dentist
dub build

Developer Notes

# run the program for development
dub run -- ARGS...

# run tests
dub test

# clean up
dub clean

Functional Description

TODO

Difficulties

Low Complexity Regions/Repeats

  1. Low Complexity Regions
    ccgcacctcaaatcgtcaccgttgtgtatcgaggggacttatagtgc
    tcctgtgacatgtcactgttgcggtcgaaccggtcgtgcaatccgac
    gtcccaatgcccgccgcattaacggtagccatAAAAAAAAAAAAAAA
    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAcgc
    atcaccgatcggggtcggtaataaaaggacaaagttagtgttggcca
    cgaacttctcacgaataagttccctggttttgcgagggaatgcatct
    gctaggcgtcactggacacagtgggaaagctgccgggggcga
    
  2. Low Complexity Regions
    ccgcacctcaaatcgtcaccgttgtgtatcgaggggacttatagtgc
    tcctgtgacatgtcAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGT
    AGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAG
    TAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTccacgagctggag
    cctaaaacaattccatgagactggtctaggttacgcagtgtagccgc
    atcaccgatcggggtcggtaataaaaggacaaagttagtgttggcca
    cgaacttctcacgaataagttccctggttttgcgagggaatgcatct
    gctaggcgtcactggacacagtgggaaagctgccgggggcga
    
  3. Tandem Repeats
    ccgcacctcaaatcgtcaccgttgtgtatcgaggggacttatagtgc
    tcctgtgacatgtcactgttgcggtcgTTGTGTATCGAGGGGACTTA
    TAGTGCTCCTGTTTGTGTATCGAGGGGACTTATAGTGCTCCTGTTTG
    TGTATCGAGGGGACTTATAGTGCTCCTGTTTGTGTATCGAGGGGACT
    TATAGTGCTCCTGTTTGTGTATCGAGGGGACTTATAGTGCTCCTGTT
    TGTGTATCGAGGGGACTTATAGTGCTCCTGTTTGTGTATCGAGGGGA
    CTTATAGTGCTCCTGTaagttccctggttttgcgagggaatgcatct
    gctaggcgtcactggacacagtgggaaagctgccgggggcga
    
  4. Transposable elements
    ccgcacctcaaatcgtcaccgttgtgtatcgaggggacttatagtgc
    tcctgtGACATGTCACTGTTGCGGTCGAACCGGTCGTGcaatccgac
    gtcccaatgcccgccgcattaacggtagccataGACATGTCACTGTT
    GCGGTCGAACCGGTCGTGtagcgcgacaaaaaccccacgagctggag
    cctaaaacaattccatgagactggtctaggGACATGTCACTGTTGCG
    GTCGAACCGGTCGTGtcgtaaaggtctgtcatagtttgtgtgtgtga
    gcggaagtataaacgaaaagaggaccagaaaaGACATGTCACTGTTG
    CGGTCGAACCGGTCGTGacagtgggaaagctgccgggggcga
    

License

This project is licensed under MIT License.

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