dentist 0.0.0

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


To use this package, run the following command in your project's root directory:

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
  1. Tandem Repeats
   ccgcacctcaaatcgtcaccgttgtgtatcgaggggacttatagtgc
   tcctgtgacatgtcactgttgcggtcgTTGTGTATCGAGGGGACTTA
   TAGTGCTCCTGTTTGTGTATCGAGGGGACTTATAGTGCTCCTGTTTG
   TGTATCGAGGGGACTTATAGTGCTCCTGTTTGTGTATCGAGGGGACT
   TATAGTGCTCCTGTTTGTGTATCGAGGGGACTTATAGTGCTCCTGTT
   TGTGTATCGAGGGGACTTATAGTGCTCCTGTTTGTGTATCGAGGGGA
   CTTATAGTGCTCCTGTaagttccctggttttgcgagggaatgcatct
   gctaggcgtcactggacacagtgggaaagctgccgggggcga
  1. Transposable elements
   ccgcacctcaaatcgtcaccgttgtgtatcgaggggacttatagtgc
   tcctgtGACATGTCACTGTTGCGGTCGAACCGGTCGTGcaatccgac
   gtcccaatgcccgccgcattaacggtagccataGACATGTCACTGTT
   GCGGTCGAACCGGTCGTGtagcgcgacaaaaaccccacgagctggag
   cctaaaacaattccatgagactggtctaggGACATGTCACTGTTGCG
   GTCGAACCGGTCGTGtcgtaaaggtctgtcatagtttgtgtgtgtga
   gcggaagtataaacgaaaagaggaccagaaaaGACATGTCACTGTTG
   CGGTCGAACCGGTCGTGacagtgggaaagctgccgggggcga

License

This project is licensed under MIT License.

Authors:
  • Arne Ludwig <arne.ludwig@posteo.de>
Dependencies:
darg, dstats, string-transform-d, vibe-d:data
Versions:
0.0.1 2019-Jan-03
0.0.1-rc.1 2018-Oct-15
0.0.1-rc.0 2018-Aug-22
0.0.0 2018-Aug-13
~master 2019-Jan-03
Show all 8 versions
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Score:
0.6
Short URL:
dentist.dub.pm