A snakemake pipeline for nanopore whole genome sequencing structural variant analysis.
Contributions welcome!
- ngmlr
- sniffles
- LAST and last-train
- minimap2
- NanoSV
- svim
- pbsv
- npInv
- tandem-genotypes
- survivor
- mosdepth
- cyvcf2
- vcfanno
- vcftools
- samtools
- matplotlib
- seaborn
Conda environment files containing the dependencies can be found in the envs directory. These can be automatically installed and managed by providing the --use-conda argument to snakemake: snakemake --use-conda ....
- 'fast': minimap2 alignment with Sniffles and SVIM SV calling
- 'precise': ngmlr alignment with Sniffles SV calling
- 'minimap2': minimap2 alignment with Sniffles, SVIM, NanoSV and npInv SV calling
- 'minimap2_pbsv': minimap2 alignment with pbsv-specific parameters with pbsv, SVIM, NanoSV and npInv SV calling
- 'ngmlr': ngmlr with Sniffles, NanoSV, SVIM and npInv SV calling
- 'last-prepare': create a LAST index and train aligner parameters using last-train
- 'last': LAST alignment with tandem-genotypes STR calling
The folder "scripts" contains scripts necessary for the pipeline.
The folder "extra_scripts" contains scripts I wrote while playing around with the results, mainly visualizations.
surpyvor: a python wrapper around SURVIVOR, with additional convenience functions for creating high sensitivity and high confidence variant sets, calculating precision and recall metrics and visualizations using venn and upset plots.
Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome