Nextflow Modules
Showing module(s) with keyword "sv"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/cutesv | Process | cutesv structural-variant calling sv | structural-variant calling with cutesv |
| nf-core/dysgu/run | Process | structural variants sv vcf | Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations. |
| nf-core/octopusv/clean | Process | vcf sv structural-variants clean harmonization | Clean broken VCF/SVCF files using OctopuSV clean |
| nf-core/octopusv/correct | Process | structural variant sv svcf normalize | Standardize a caller VCF into OctopuSV SVCF format. |
| nf-core/octopusv/filter | Process | structural variant sv svcf filter | Filter SVCF based on specified criteria |
| nf-core/octopusv/subset | Process | structural variant sv svcf subset | Subset an OctopuSV SVCF by sample and/or caller. |
| nf-core/strvctvre/strvctvre | Process | structural variants sv deletions duplications annotations | a structural variant classifier for exonic deletions and duplications |
| nf-core/survivor/simsv | Process | structural variants simulation sv vcf | Simulate an SV VCF file based on a reference genome |
| nf-core/svaba | Process | sv structural variants detecting svs short-read sequencing | SvABA is an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements |
| nf-core/svanalyzer/svbenchmark | Process | structural variant sv benchmarking | SVbenchmark compares a set of “test” structural variants in VCF format to a known truth set (also in VCF format) and outputs estimates of sensitivity and specificity. |
| nf-core/svtyper/svtyper | Process | sv structural variants genotyping | SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data |
| nf-core/svtyper/svtypersso | Process | sv structural variants genotyping Bayesian | SVTyper-sso computes structural variant (SV) genotypes based on breakpoint depth on a SINGLE sample |
| nf-core/svync | Process | structural variants vcf standardization standardize sv | A tool to standardize VCF files from structural variant callers |
| nf-core/truvari/bench | Process | structural variants sv vcf benchmark comparison | Given baseline and comparison sets of variants, calculate the recall/precision/f-measure |
| nf-core/truvari/consistency | Process | structural variants sv vcf intersection comparison | Over multiple vcfs, calculate their intersection/consistency. |
| nf-core/truvari/segment | Process | structural variants sv vcf benchmark normalization | Normalization of SVs into disjointed genomic regions |
| nf-core/vardictjava | Process | variant calling vcf bam snv sv | The Java port of the VarDict variant caller |