Structural variant calling from single-cell Strand-seq data Snakemake pipeline.
MosaiCatcher-pipeline
This workflow uses Snakemake to execute all steps of MosaiCatcher in order. The starting point are single-cell BAM files from Strand-seq experiments and the final output are SV predictions in a tabular format as well as in a graphical representation. To get to this point, the workflow goes through the following steps:
- Binning of sequencing reads in genomic windows of 200kb via mosaic
- Strand state detection
- [Optional]Normalization of coverage with respect to a reference sample
- Multi-variate segmentation of cells (mosaic)
- Haplotype resolution via StrandPhaseR
- Bayesian classification of segmentation to find SVs using MosaiClassifier
- Visualization of results using custom R plots
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| MosaiCatcher snakemake pipeline and visualisations examples |
| ashleys-qc-pipeline |
Documentation
📚 Homepage: https://friendsofstrandseq.github.io/mosaicatcher-docs/
💂♂️ Authors (alphabetical order)
- Ashraf Hufash
- Cosenza Marco
- Ebert Peter
- Ghareghani Maryam
- Grimes Karen
- Gros Christina
- Höps Wolfram
- Jeong Hyobin
- Kinanen Venla
- Korbel Jan
- Marschall Tobias
- Meiers Sasha
- Porubsky David
- Rausch Tobias
- Sanders Ashley
- Van Vliet Alex
- Weber Thomas (maintainer and current developer)
Citing MosaiCatcher
When using MosaiCatcher for a publication, please cite the following article in your paper:
📕 References
MosaiCatcher v2 publication: Weber Thomas, Marco Raffaele Cosenza, and Jan Korbel. 2023. ‘MosaiCatcher v2: A Single-Cell Structural Variations Detection and Analysis Reference Framework Based on Strand-Seq’. Bioinformatics 39 (11): btad633. https://doi.org/10.1093/bioinformatics/btad633.
Strand-seq publication: Falconer, E., Hills, M., Naumann, U. et al. DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution. Nat Methods 9, 1107–1112 (2012). https://doi.org/10.1038/nmeth.2206
scTRIP/MosaiCatcher original publication: Sanders, A.D., Meiers, S., Ghareghani, M. et al. Single-cell analysis of structural variations and complex rearrangements with tri-channel processing. Nat Biotechnol 38, 343–354 (2020). https://doi.org/10.1038/s41587-019-0366-x
ArbiGent publication: Porubsky, David, Wolfram Höps, Hufsah Ashraf, PingHsun Hsieh, Bernardo Rodriguez-Martin, Feyza Yilmaz, Jana Ebler, et al. 2022. “Recurrent Inversion Polymorphisms in Humans Associate with Genetic Instability and Genomic Disorders.” Cell 185 (11): 1986-2005.e26. https://doi.org/10.1016/j.cell.2022.04.017.
scNOVA publication: Jeong, Hyobin, Karen Grimes, Kerstin K. Rauwolf, Peter-Martin Bruch, Tobias Rausch, Patrick Hasenfeld, Eva Benito, et al. 2022. “Functional Analysis of Structural Variants in Single Cells Using Strand-Seq.” Nature Biotechnology, November, 1–13. https://doi.org/10.1038/s41587-022-01551-4.