---
# System prepended metadata

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

---

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

# nf-core/genomeassembler assembly validation and curation discussion

## Desired components:

- K-mer copy number spectra profile - Merqury
- Contamination profile - Blobtools
- Gene space checks - Busco ( Dogma too?)
- Assembly comparison and stats - Quast
- Other accuracy metrics ( Inspector ? FRCBam ? )
- Pairwise genome plots
- Assembly graph plots ( Bandage )
- Read coverage ( Qualimap, Blobtools )
- Output genome browser tracks with useful information, like polished areas, missassembly signals, coverage, etc

## Workflow diagram draft:

```mermaid
flowchart LR
  Assemblies --> Quast
  Assemblies --> BUSCO
  Assemblies --> on-demand:Bakta
  Assemblies --> Merqury
  PacBioHifi --> Merqury
```

## Implementations:

- [Pairwise genome comparison workflow](https://github.com/oist/plessy_pairwiseGenomeComparison)
- Generate list of pairwise inputs:
  ```nextflow
  workflow {
    Channel.of( 'A', 'B', 'C' )
        .toSortedList()
        .flatMap {
            it.subsequences()
                .findAll { it.size() == 2 }
        }.view()
    // Output is [B, C], [A, B], [A, C]
  }
  ```