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
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
- Low Complexity Regions
ccgcacctcaaatcgtcaccgttgtgtatcgaggggacttatagtgc tcctgtgacatgtcactgttgcggtcgaaccggtcgtgcaatccgac gtcccaatgcccgccgcattaacggtagccatAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAcgc atcaccgatcggggtcggtaataaaaggacaaagttagtgttggcca cgaacttctcacgaataagttccctggttttgcgagggaatgcatct gctaggcgtcactggacacagtgggaaagctgccgggggcga
- Low Complexity Regions
ccgcacctcaaatcgtcaccgttgtgtatcgaggggacttatagtgc
tcctgtgacatgtcAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGT
AGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAG
TAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTccacgagctggag
cctaaaacaattccatgagactggtctaggttacgcagtgtagccgc
atcaccgatcggggtcggtaataaaaggacaaagttagtgttggcca
cgaacttctcacgaataagttccctggttttgcgagggaatgcatct
gctaggcgtcactggacacagtgggaaagctgccgggggcga
- Tandem Repeats
ccgcacctcaaatcgtcaccgttgtgtatcgaggggacttatagtgc
tcctgtgacatgtcactgttgcggtcgTTGTGTATCGAGGGGACTTA
TAGTGCTCCTGTTTGTGTATCGAGGGGACTTATAGTGCTCCTGTTTG
TGTATCGAGGGGACTTATAGTGCTCCTGTTTGTGTATCGAGGGGACT
TATAGTGCTCCTGTTTGTGTATCGAGGGGACTTATAGTGCTCCTGTT
TGTGTATCGAGGGGACTTATAGTGCTCCTGTTTGTGTATCGAGGGGA
CTTATAGTGCTCCTGTaagttccctggttttgcgagggaatgcatct
gctaggcgtcactggacacagtgggaaagctgccgggggcga
- Transposable elements
ccgcacctcaaatcgtcaccgttgtgtatcgaggggacttatagtgc
tcctgtGACATGTCACTGTTGCGGTCGAACCGGTCGTGcaatccgac
gtcccaatgcccgccgcattaacggtagccataGACATGTCACTGTT
GCGGTCGAACCGGTCGTGtagcgcgacaaaaaccccacgagctggag
cctaaaacaattccatgagactggtctaggGACATGTCACTGTTGCG
GTCGAACCGGTCGTGtcgtaaaggtctgtcatagtttgtgtgtgtga
gcggaagtataaacgaaaagaggaccagaaaaGACATGTCACTGTTG
CGGTCGAACCGGTCGTGacagtgggaaagctgccgggggcga
License
This project is licensed under MIT License.
- 0.0.1 released a month ago
- a-ludi/dentist
- MIT
- Copyright © 2018, Arne Ludwig <arne.ludwig@posteo.de>
- Authors:
- 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 - Download Stats:
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- Score:
- 0.4
- Short URL:
- dentist.dub.pm