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nanopore-sv-evaluation

This is the code repository for the paper "Evaluating nanopore sequencing data processing pipelines for structure variation identification".

• scripts/download.sh: code for downloading the online data

• scripts/simulation.sh: code for genreating simulation datasets

• scripts/workflow.sh: code for running the aligners and SV callers

• scripts/integration.sh: code for consensus call set generation

• scripts/comparison.md: code for call set and true set comparisons

• scripts/coverage.sh: code for subsetting the reads and coverages analysis

• scripts/ML/gen_label.sh: code for generating labels for the random forest classifier

• scripts/ML/random_forest.py: code for the random forest classifier training, predicting, and evaluating