Assembly

Assembly subworkflow

The basic workflow is to take the filtered Nanopore reads, assemble them, evaluate draft genomes with gfastats, and rotate the closed sequences with circlator.

There are several assemblers included in Donut Falls

• flye (params.assembler = 'flye')
• raven (params.assembler = 'raven')
• miniasm and minipolish (params.assembler = 'miniasm')
• unicycler (params.assembler = 'lr_unicycler')

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Donut Falls
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flowchart LR

A[filtered fastq] --> B[assembly]
B --> C[gfastats]
B --> F[Bandage]
C --> D[circlator]
D --> E[consensus fasta]

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Relevant parameters (params) and their default values

params.assembler          = 'flye' // or 'raven' or 'miniasm' or 'lr_unicycler' or 'dragonflye'
params.bandage_options    = ''
params.circlator_options  = ''
params.dragonflye_options = ''
params.flye_options       = ''
params.gfastats_options   = ''
params.raven_options      = '--polishing-rounds 2'
params.unicycler_options  = ''