Assembly

subworkflows/local/assemble_reads

NOTE: Hybrid assembly of long and short reads uses a different workflow that can be found here

Steps

1. Assembly proceeds differently depending whether paired-end short or long reads. If the samples are marked as metagenomic, then metagenomic assembly flags will be added to the corresponding assembler.
2. Paired end assembly is performed using Spades (for more information see the module spades_assemble.nf)

3. Long read assembly is performed using Flye (for more information see the module flye_assemble.nf

4. Bandage plots are generated using Bandage, these images were included as they can be informative of assembly quality in some situations bandage_image.nf.

5. Polishing (OPTIONAL) can be performed on either short or long/hybrid assemblies. Minimap2 is used to create a contig index minimap2_index.nf and then maps reads to that index minimap2_map.nf. Lastly, Racon uses this output to perform contig polishing racon_polish.nf. To turn off polishing add the following to your command line parameters --skip_polishing.

Input

• Processed Reads from clean reads subworkflow

Output

• Reads
• FinalReads
  • SAMPLE
• Processing
  • Dehosting
  • Trimmed
    • FastP
    • MashSketches