EValuation of Nanopore (SV) Callers
Evaluation of the performances of long-read structural variant (SV) callers on long reads from Oxford Nanopore Technologies. This will include tests both on real and simulated datasets.
To date, the following methods (versions) are tested:
Long-read aligners tested:
Other tools used by the pipeline:
- samtools (1.9), using htslib (1.9)
- bcftools (1.9), using htslib (1.9)
- truvari (2.0.0-dev)
- SURVIVOR (1.0.7)
- VISOR (1.1)
Pipelines are built using Snakemake to improve readability/reproducibility of the results. This also allows to install most of the tools required for each command on-the-fly, using the --use-conda flag.
Are you using EViNCe in your works? Please cite:
Davide Bolognini, Alberto Magi. Evaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data. Front Genet. 2021 Nov 18.