Canu

Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).

Canu is a hierarchical assembly pipeline which runs in four steps:

• Detect overlaps in high-noise sequences using MHAP
• Generate corrected sequence consensus
• Trim corrected sequences
• Assemble trimmed corrected sequences

Citation:

• Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research. (2017).

How to run My-Toil-Canu:

    git clone https://github.com/reihaneh-torkzadehmahani/canu.git
    sudo chmod 755 ./canu/RunScript.sh
    cd canu
    ./RunScript.sh
  
    cd Linux-amd64/bin/
    python ToilCanu.py -c """/home/ubuntu/canu/Linux-amd64/bin/""" -o '-p ecoli -d ecoil-oxford2 genomeSize=4.8m corMinCoverage=0 corMaxEvidenceErate=0.22 "corMhapOptions=--threshold 0.8 --num-hashes 512 --ordered-sketch-size 1000 --ordered-kmer-size 14"  -nanopore-raw oxford.fasta'