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Clean Assemble

workflows/local/CleanAssemble

Included sub-workflows

  • assemble_reads.nf
  • clean_reads.nf
  • hybrid_assembly.nf
  • input_check.nf
  • polish_assemblies.nf

Steps

  1. QC reads subworkflow steps in brief are listed below, for further information see clean_reads.nf

    • Reads are checked for known sequencing contamination
    • Quality metrics are calculated
    • Reads are trimmed
    • Coverage is estimated
    • Read set subsampled to set level (OPTIONAL)
    • Read set is assessed to be either an isolate or metagenomic sample (from presence of multiple taxa)

  2. Assemble reads using the params.platform flag, read sets will be diverted to either the assemble_reads (short reads) or hybrid_assembly (short and/or long reads) workflow. Though the data is handled differently in eash subworklow, both generate a contigs file and a bandage image, with an option of initial polishing via Racon. See assemble_reads.nf and hybrid_assembly.nf subworkflow pages for more details.

  3. Polish assembles (OPTIONAL) Polishing of contigs can be added polish_assemblies.nf. To make changes to the default workflow, see setting 'optional flags' page.

Input

  • Next generation sequencing reads:
    • Short read - Illumina
    • Long read:
      • Nanopore
      • Pacbio

Output

  • Reads
  • FinalReads
    • SAMPLE
  • Processing
    • Dehosting
      • Trimmed
        • FastP
        • MashSketches
  • Quality
    • RawReadQuality
    • Trimmed
      • FastP
      • MashScreen
  • Assembly
    • Assembling
      • Bandage
      • ConsensusGeneration
        • Polishing
          • Pilon
            • BAMs
            • Changes
            • Fasta
            • VCF
        • Racon
          • Consensus
      • Spades
        • Contigs
        • GeneClusters
        • Graphs
        • Logs
        • Scaffolds
        • Transcripts
    • FinalAssembly
      • SAMPLE

NOTE: Bolded directories contain the nested structure of tool output. The further into the structure you go, the further along the workflow that that tool was run.