Bash scripting to generate genomic single nucleotide polymorphisms (SNPs).

Overview

This workflow was modified (1-5) to use short-read seqences from genomic DNA isolates of Phytophthora cinnamomi, a soil-bourne water mould, for SNP discovery and isolate comparisons. Bash scripts are used in numeric order to process these data as a workflow.

Requirements

Environment

Linux or something that can run command line programs through a bash shell.

Software

• SRA Toolkit (6)
• FastQC (7)
• MultiQC (8)
• Trimmomatic (9)
• SAMtools/BCFtools (10-11)
• BWA-MEM (12)
• BEDTools (13)
• Picard toolkit (14)
• ANGSD (15)

Published data

• Reference genome is available from JGI (16)
• Phytophtera resequenced genomes NCBI (17)
• Phytophtera SNP dataset GBS-Pcinnamomi
• Novel data for this study was produced at Genome Quebec and is coming soon to NCBI!

Workflow overview

1. Download published data
2. QC reads (scripts 1 & 2)
3. Trim reads (script 2 & NEBnext_dual.fasta)
4. Repeat step 2
5. Read mapping (scripts 4-11)
6. Calling SNPs (scripts 12-17)
7. Extracting specific SNPs (script 18)

References

1. Poplin et al. 2017. Biorxiv, 201178.
2. Van Der Auwera et al. 2013. Current Protocols in Bioinformatics 43 (1). https://doi.org/10.1002/0471250953.bi1110s43.
3. Van der Auwera et al. 2020. O’Reilly Media. ISBN: 9781491975190.
4. Fraser et al. 2020. Genome Biology and Evolution 12 (10):1789–805. https://doi.org/10.1093/gbe/evaa187.
5. Moran et al. 2023. Nature Communications 14 (1): 2557. https://doi.org/10.1038/s41467-023-37909-8.
6. SRA Toolkit Development Team. https://github.com/ncbi/sra-tools
7. Babraham Bioinformatics. 2024. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
8. Ewels et al. 2016. Bioinformatics 32 (19): 3047–48. https://doi.org/10.1093/bioinformatics/btw354.
9. Bolger et al. 2014. Bioinformatics 30 (15): 2114–20. https://doi.org/10.1093/bioinformatics/btu170.
10. Danecek et al. 2021. GigaScience 10 (2):giab008. https://doi.org/10.1093/gigascience/giab008.
11. Li et al. 2009. Bioinformatics 25 (16):2078–79. https://doi.org/10.1093/bioinformatics/btp352.
12. Vasimuddin et al. 2019. 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), May, 314–24. https://doi.org/10.1109/IPDPS.2019.00041.
13. Quinlan and Hall. 2010. Bioinformatics 26 (6): 841–42. https://doi.org/10.1093/bioinformatics/btq033.
14. “Picard Toolkit.” 2019. Broad Institute. https://broadinstitute.github.io/picard/
15. Korneliussen et al. 2014. BMC Bioinformatics 15 (1): 356. https://doi.org/10.1186/s12859-014-0356-4.
16. Shakya et al. 2021. Molecular Ecology 30 (20): 5164–78. https://doi.org/10.1111/mec.16109.
17. McDougal et al. 2025. Data in Brief 60 (June): 111655. https://doi.org/10.1016/j.dib.2025.111655.

Contact

Rhiannon Peery: rhiannon.peery@nrcan-rncan.gc.ca

License

The first available version of the workflow "Variant calling workflow for short-read genome resequencing" was developed by Natural Resources Canada and is licensed under CC BY-NC 4.0

© His Majesty the King in Right of Canada, as represented by the Minister of Natural Resources, 2026.
© Sa Majesté le Roi du Canada, représentée par le ministre des Ressources naturelles, 2026.