README.md

plant-food-research-open/assemblyqc

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. The pipeline includes skip flags to disable execution of various tools.

Pipeline Flowchart

• Assembly
  • fasta_validator + SeqKit rmdup: FASTA validation
  • assemblathon_stats, gfastats: Assembly statistics
  • NCBI FCS-adaptor: Adaptor contamination pass/fail
  • NCBI FCS-GX: Foreign organism contamination pass/fail
  • tidk: Telomere repeat identification
  • BUSCO: Gene-space completeness estimation
  • LAI: Continuity of repetitive sequences
  • Kraken 2, Krona: Taxonomy classification
  • Alignment and visualisation of HiC data
    • sra-tools: HiC data download from SRA or use of local FASTQ files
    • fastp, FastQC: Read QC and trimming
    • SeqKit sort: Alphanumeric sorting of FASTA by sequence ID
    • bwa-mem: HiC read alignment
    • samblaster: Duplicate marking
    • hic_qc: HiC read and alignment statistics
    • Matlock: BAM to juicer conversion
    • 3d-dna/visualize: .hic file creation
    • juicebox.js: HiC contact map visualisation
  • K-mer completeness, consensus quality and phasing assessment
    • sra-tools: Assembly, maternal and paternal data download from SRA or use of local FASTQ files
    • Merqury hapmers: Hapmer generation if parental data is available
    • Merqury: Completeness, consensus quality and phasing assessment
  • Synteny analysis
    • MUMmer → Circos + dotplot: One-to-all and all-to-all synteny analysis at the contig level
    • Minimap2 → Syri/Plotsr: One-to-one synteny analysis at the chromosome level
• Annotation
  • GenomeTools gt gff3validator + FASTA/GFF correspondence: GFF3 validation
  • GenomeTools gt stat: Annotation statistics
  • GffRead, BUSCO: Gene-space completeness estimation in annotation proteins
  • OrthoFinder: Phylogenetic orthology inference for comparative genomics

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 \
  -revision <version> \
  -profile <docker/singularity/.../institute> \
  --input assemblysheet.csv \
  --outdir <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) and Simon Pearce (@SPPearce) 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:

AssemblyQC: A Nextflow pipeline for reproducible reporting of assembly quality.

Usman Rashid, Chen Wu, Jason Shiller, Ken Smith, Ross Crowhurst, Marcus Davy, Ting-Hsuan Chen, Ignacio Carvajal, Sarah Bailey, Susan Thomson & Cecilia H Deng.

Bioinformatics. 2024 July 30. doi: 10.1093/bioinformatics/btae477.

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.