---
# System prepended metadata

title: nf-core/genomeassembler assembly workflow planning
tags: [plans, pipeline, genomeassembler, planning]

---

---
title: "nf-core/genomeassembler assembly workflow planning"
tags: pipeline,genomeassembler,planning,plans
---

# nf-core/genomeassembler assembly workflow discussion

## Desired components:

- assembles
- polishes
- scaffolds
- purge_dups
- phases
- sub assembly of organelles, sex chromosomes, germline/somatic genomes (https://www.nature.com/articles/s41467-019-13427-4)
- circular DNA rotation ( e.g., plasmids, organelles, etc )

## Workflow diagram draft:

Are Tricycler & SPAdes prokaryote specific?

```mermaid
flowchart LR
  Illumina-WGS --> SPAdes
  Illumina-WGS --> Shovill
  Illumina-WGS --> Shovill-SE
  SPAdes --> Illumina-Output
  Shovill --> Illumina-Output
  Shovill-SE --> Illumina-Output  
```

```mermaid
flowchart LR
  PacBioHifi --> Canu
  PacBioHifi --> HiFiAsm
  PacBioHifi --> Flye
  Canu --> Pacbio-Output
  Flye --> Pacbio-Output
  HiFiAsm --> Pacbio-Output
```

```mermaid
flowchart LR
  Illumina-WGS --> Pilon
  Nanopore --> Canu
  Nanopore --> RedBean
  Nanopore --> Raven
  Nanopore --> Shasta
  Nanopore --> Miniasm
  Nanopore --> Flye
  Canu --> Tricycler
  Flye --> Tricycler
  RedBean --> Tricycler
  Raven --> Tricycler
  Shasta --> Tricycler
  Miniasm --> Tricycler
  Tricycler --> Medaka
  Tricycler --> Pilon
  Tricycler --> NanoPolish
  Nanopore-fast5 --> NanoPolish
  NanoPolish --> Nanopore-Output
  Pilon --> Nanopore-Output
  Medaka --> Nanopore-Output
```

<!-- Felipe Almeida: I am making some change suggestions here in the graph as I believe some processes are not fit.
     1. PacBioHifi I believe should not be passed to spades. I believe the tools that handles them best are hifiasm, flye and canu.
     2. I believe the graph should use Tricycler as a consensus maker as it gets generated assemblies and creates a consensus instead of having "Nanopore -> Tricycler" we must "Canu -> Tricycler"
     3. I don't believe tricycler can be used for short reads.
     4. Tricycler output can be polished later with Medaka or Pilon. Tricycler expects "raw" assemblies.
     5. I believe saying the generated end-line of each workflow in the graph should help understanding it. E.g "Pacbio-Output".
     6. Maybe is better to separate graphs for cleaner visualization?

I left the removed lines in the mermaid graph below:
  Illumina-WGS -\-> Tricycler
  PacBioHifi -\-> SPAdes
  PacBioHifi -\-> Tricycler
  Nanopore -\-> SPAdes
  Nanopore -\-> Tricycler
  Miniasm -\-> Racon
  Racon -\-> NanoPolish
  Racon -\-> Medaka
-->