---
# System prepended metadata

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

---

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

# nf-core/genomeassembler planning

A document to design and build the nf-core/genomeassembler workflow. Please add your input below. 

- What functionality would you like to support?

## How to contribute 

This is a community project and we would like to hear your input. Join the discussion on [Slack](https://nfcore.slack.com/channels/genomeassembler) and help record decisions here.

### Coding together 

How nf-core works:

- All tools to be included in a workflow should ideally be on [nf-core modules](https://github.com/nf-core/modules/) (but some could also be "local" modules).
- Discussions about what to implement happen on [Slack](https://nfcore.slack.com/channels/genomeassembler).
- Code is written and submitted as a pull request to the `dev` branch, where it is reviewed by another member of the community (does not have to be core-team). 
- A new pipeline like this will have a pseudo pull request, where the community can review the whole before a release is made.

How this collaboration could work in practice:

1. Discuss what we want to implement, and record any final decisions here (with mermaid diagram of what we want implemented).
2. Make an issue on the [Github repo](https://github.com/nf-core/genomeassembler/issues) with a mermaid diagram of the subworkflow to be implemented, and assign someone to be in charge of it. Make a list of modules that need to be implemented, and ask for help contributing said modules to the [nf-core modules repository](https://github.com/nf-core/modules/). Once the person in charge of the subworkflow has checked off all the modules, they can be chained together and a pull request made.
3. Make sure it all works with the test profile.

## Scope

### Functionality

- Genome assembly raw data inspection and preprocessing
- Genome assembly
- Genome assembly validation and curation
- Draft gene annotation, possibly not default

### Data types

- Illumina
    - PE!, also SE?
    - fastq
    - artificial long reads, such as [TELL-Seq](https://www.universalsequencing.com/technology)?
- PacBio Hifi
    - Bam
    - Fastq
- Oxford Nanopore ( chemistry? )
    - fastq
    - fast5
- Hi-C
- Draft assemblies
    - Consensus
    - Phased
    - Genome graph?

### What can be analysed:

- Whole genome sequencing
- Whole genome amplified?
- Low DNA input?

## Implementation

- [How to supply workflow parameters](/du0qz4T_R-yHFHQWjy21MQ)
- [Testing datasets](/uXe7WQcPTiqtlxfgQ4hUNw)
- [Genome assembly raw data QC process](/yWMNKLYHRKqZNEvGKbCvjg)
- [Genome assembly process](/4A0sNjXPRTaSckeSIKfR1A)
- [Genome assembly post-processing](/WPFwzJx0STqG-gJBXkX8CQ)

Assembling a high quality genome is an iterative process.

```mermaid
flowchart TD
  preassembly( Genome assembly raw data QC) --> assembly( Genome assembly )
  assembly --> preassembly
  assembly --> postassembly( Genome assembly validation and curation )
  postassembly --> assembly
```

## Resources

- [Markdown tutorial](https://www.markdowntutorial.com/)
- [Markdown Syntax Reference](/9iTFcssSTZ-f24wmhbXUNw)
- [Mermaid syntax](https://mermaid-js.github.io/mermaid/#/)

## References

- [Significantly improving the quality of genome assemblies through curation](https://pubmed.ncbi.nlm.nih.gov/33420778/).
