---
# System prepended metadata

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

---

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

# nf-core/genomeassembler data QC and preprocessing discussion

## Desired components:

### Quality Checks:

- Check file checksums
- FastQC / Nanoplot / etc
- Kraken2 / Mash
- K-mer histogram ( GenomeScope )
- K-mer consistency between files ( i.e. seeing biases between different files cf. https://kat.readthedocs.io/en/latest/walkthrough.html#checking-library-consistency )
- Data quantity check.
- Read chimerism.

### Preprocessing:

- Adapter removal
    - [HiFiAdapterFilt](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08375-1)
- Subsampling
- Normalization (e.g. for Whole genome amplified)
- Read filtering 
    - from List (txt file)
    - from mapping (take ID's from bam)

## Workflow diagram draft:

```mermaid
flowchart LR
  Illumina-WGS --> FastQC
  Hi-C --> FastQC
  Nanopore --> Nanoplot
  Nanopore --> PycoQC
  PacBioHifi --> Nanoplot
  Illumina-WGS --> Kraken2/Mash
  PacBioHifi --> Kraken2/Mash
  Nanopore --> Kraken2/Mash
```