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
%%{init: {
'theme': 'base',
'themeVariables': {
'fontSize': '52px",
'primaryColor': '#9A6421',
'primaryTextColor': '#ffffff',
'primaryBorderColor': '#9A6421',
'lineColor': '#B180A8',
'secondaryColor': '#455C58',
'tertiaryColor': '#ffffff'
}
}}%%
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 reportfasta:
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:
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.
Version History
main @ 690e56b (earliest) Created 25th Jun 2024 at 02:40 by Usman Rashid
Merge pull request #89 from Plant-Food-Research-Open/dev
Candidate for 2.0.0
Frozen
main
690e56b
Creators
Submitter
Views: 1579 Downloads: 150
Created: 25th Jun 2024 at 02:40
None