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Welcome to the wiki for Donut falls!

All "good" bioinformatic tools and workflows are attempting to solve a problem. The problem we ran into was that nf-core's genomeassembler workflow was not completed, yet, and we needed a simple workflow to assembly nanopore sequencing reads with and without corresponding Illumina reads for downstream analyses.

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Donut Falls
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flowchart LR

A[nanopore fastq] --> B[filter]
B[filter] --> C[assembly]
C[assembly] --> D[polish]
D[polish] --> consensus

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Nanopore sequencing with polishing

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Donut Falls
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flowchart LR

E[nanopore fastq] --> F[filter]
G[illumina fastq] --> H[fastp]
F[filter] --> I[assembly]
I[assembly] --> J[polish]
H[fastp] --> J[polish]

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Hybrid assembly

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Donut Falls
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flowchart LR
K[nanopore fastq] --> L[assembly]
L[illumina fastq] --> L[assembly]

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