djunctor

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

Building

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

Developer Notes

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

# run tests
dub test

# clean up
dub clean

Functional Description

djunctor takes two inputs, a reference assembly and a set of long reads (PacBio) and tries to close scaffold gaps or reduce their size.

Functional Overview

program djunctor(ReferenceAssembly, LongReads)
begin
    FindAlignments()

    repeat
        FilterUselessReads()
        BuildPileUpsFromAlignments()

        for each pileUp do
            SelectGoodReads()
            BuildConsensus()
            InsertHit()
    until (numHits == 0 or maxIterationsReached)

    OutputResult()
end

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.