SVUPP: Structural Variants Genotyping Using Pre-Phased Reads

Here we uploaded the source code of relevant software and code for reproducing plots in our paper. SVUPP.zip is the Nextflow pipeline, which is hosted at https://github.com/Zilong-Li/SVUPP. SVUPP_paper.zip contains the code for all analyses and assessement of results. svupp.sif is the Sigularity image that has all dependencies, such as QUILT2 and the modified version of cuteSV2. svupp_docker.tar.gz is the Docker image that has all dependencies, such as QUILT2 and the modified version of cuteSV2. cuteSV.zip is the source code of a modified version of cuteSV v2.1.1 with our customized genotyping module.

Publication Details

Journal
Zenodo (CERN European Organization for Nuclear Research)
Published
2025-10-24
DOI
https://doi.org/10.5281/zenodo.17569072
Primary Topic
Genomics and Rare Diseases
Type
article
Field-Weighted Citation Impact
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article

SVUPP: Structural Variants Genotyping Using Pre-Phased Reads

Zenodo (CERN European Organization for Nuclear Research)
Genomics and Rare Diseases
article

SVUPP: Structural Variants Genotyping Using Pre-Phased Reads

article en

Abstract

Here we uploaded the source code of relevant software and code for reproducing plots in our paper. SVUPP.zip is the Nextflow pipeline, which is hosted at https://github.com/Zilong-Li/SVUPP. SVUPP_paper.zip contains the code for all analyses and assessement of results. svupp.sif is the Sigularity image that has all dependencies, such as QUILT2 and the modified version of cuteSV2. svupp_docker.tar.gz is the Docker image that has all dependencies, such as QUILT2 and the modified version of cuteSV2. cuteSV.zip is the source code of a modified version of cuteSV v2.1.1 with our customized genotyping module.

Zenodo (CERN European Organization for Nuclear Research)
Openalex Percentile: Top 32%
Genomics and Rare Diseases
DOIOpen Access PDFOpenAlex
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SVUPP: Structural Variants Genotyping Using Pre-Phased Reads · Zenodo (CERN European Organization for Nuclear Research) (2025) | TGRS Research Map | TGRS