dentist 0.0.1

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


To use this package, put the following dependency into your project's dependencies section:

dub.json
dub.sdl
InfoDocumentation

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, vibe-d:data, string-transform-d
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:
0.4
Short URL:
dentist.dub.pm