Hybrid Assembly

subworkflows/local/hybrid_assembly

Choice of 2 workflows

1. DEFAULT A. Flye assembly flye_assembly.nf B. Bandage creates a bandage plot of the assembly bandage_image.nf C. Minimap2 creates an index of the contigs (minimap2_index.nf), then maps long reads to this index minimap2_map.nf D. Racon uses the short reads to iteratively polish contigs pilon_iter.nf
2. OPTIONAL A. Unicycler assembly unicycler_assemble.nf B. Bandage creates a bandage plot of the assembly bandage_image.nf

Input

• Next generation sequencing reads:
  • Short read
    • Illumina
  • Long read:
    • Nanopore
    • Pacbio
• User submitted sample sheet

Output

• Assembly
  • Assembling
    • Bandage
    • ConsensusGeneration
      • Polishing
        • Pilon
          • BAMs
          • Changes
          • Fasta
          • VCF
      • Racon
        • Consensus
    • Unicycler
  • FinalAssembly
    • SAMPLE