AssemblyQC: A NextFlow pipeline for evaluating assembly quality

main @ 690e56b

Introduction

plant-food-research-open/assemblyqc is a NextFlow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report. The tools are shown in the Pipeline Flowchart and their references are listed in CITATIONS.md.

Pipeline Flowchart

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flowchart LR
  forEachTag(Assembly) ==> VALIDATE_FORMAT[VALIDATE FORMAT]

  VALIDATE_FORMAT ==> ncbiFCS[NCBI FCS\nADAPTOR]
  ncbiFCS ==> Check{Check}

  VALIDATE_FORMAT ==> ncbiGX[NCBI FCS GX]
  ncbiGX ==> Check
  Check ==> |Clean|Run(Run)

  Check ==> |Contamination|Skip(Skip All)
  Skip ==> REPORT

  VALIDATE_FORMAT ==> GFF_STATS[GENOMETOOLS GT STAT]

  Run ==> ASS_STATS[ASSEMBLATHON STATS]
  Run ==> BUSCO
  Run ==> TIDK
  Run ==> LAI
  Run ==> KRAKEN2
  Run ==> HIC_CONTACT_MAP[HIC CONTACT MAP]
  Run ==> MUMMER
  Run ==> MINIMAP2
  Run ==> MERQURY

  MUMMER ==> CIRCOS
  MUMMER ==> DOTPLOT

  MINIMAP2 ==> PLOTSR

  ASS_STATS ==> REPORT
  GFF_STATS ==> REPORT
  BUSCO ==> REPORT
  TIDK ==> REPORT
  LAI ==> REPORT
  KRAKEN2 ==> REPORT
  HIC_CONTACT_MAP ==> REPORT
  CIRCOS ==> REPORT
  DOTPLOT ==> REPORT
  PLOTSR ==> REPORT
  MERQURY ==> REPORT

• FASTA VALIDATOR + SEQKIT RMDUP: FASTA validation
• GENOMETOOLS GT GFF3VALIDATOR: GFF3 validation
• ASSEMBLATHON STATS: Assembly statistics
• GENOMETOOLS GT STAT: Annotation statistics
• NCBI FCS ADAPTOR: Adaptor contamination pass/fail
• NCBI FCS GX: Foreign organism contamination pass/fail
• BUSCO: Gene-space completeness estimation
• TIDK: Telomere repeat identification
• LAI: Continuity of repetitive sequences
• KRAKEN2: Taxonomy classification
• HIC CONTACT MAP: Alignment and visualisation of HiC data
• MUMMER → CIRCOS + DOTPLOT & MINIMAP2 → PLOTSR: Synteny analysis
• MERQURY: K-mer completeness, consensus quality and phasing assessment

Usage

Refer to usage, parameters and output documents for details.

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Prepare an assemblysheet.csv file with following columns representing target assemblies and associated meta-data.

• tag: A unique tag which represents the target assembly throughout the pipeline and in the final report
• fasta: FASTA file

Now, you can run the pipeline using:

nextflow run plant-food-research-open/assemblyqc \
   -profile  \
   --input assemblysheet.csv \
   --outdir 

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Plant&Food Users

Download the pipeline to your /workspace/$USER folder. Change the parameters defined in the pfr/params.json file. Submit the pipeline to SLURM for execution.

sbatch ./pfr_assemblyqc

Credits

plant-food-research-open/assemblyqc was originally written by Usman Rashid (@gallvp) and Ken Smith (@hzlnutspread).

Ross Crowhurst (@rosscrowhurst), Chen Wu (@christinawu2008) and Marcus Davy (@mdavy86) generously contributed their QC scripts.

Mahesh Binzer-Panchal (@mahesh-panchal) helped port the pipeline modules and sub-workflows to nf-core schema.

We thank the following people for their extensive assistance in the development of this pipeline:

• Cecilia Deng
• Ignacio Carvajal
• Jason Shiller
• Sarah Bailey
• Susan Thomson
• Ting-Hsuan Chen

The pipeline uses nf-core modules contributed by following authors:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

If you use plant-food-research-open/assemblyqc for your analysis, please cite it as:

Rashid, U., Wu, C., Shiller, J., Smith, K., Crowhurst, R., Davy, M., Chen, T.-H., Thomson, S., & Deng, C. (2024). AssemblyQC: A NextFlow pipeline for evaluating assembly quality (2.0.0). Zenodo. https://doi.org/10.5281/zenodo.10647870

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.