Nextflow Modules
Showing module(s) with keyword "benchmarking"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/aardvark/compare | Process | variant calling benchmarking vcf comparison consensus | A tool to evaluate variant calling performance by comparing a query VCF against a truth VCF. |
| nf-core/holodeck/eval | Process | simulation evaluation alignment accuracy benchmarking | Evaluate alignment accuracy of holodeck-simulated reads |
| nf-core/holodeck/methylate | Process | simulation vcf methylation bisulfite benchmarking | Generate a methylation-annotated VCF from a reference genome with holodeck |
| nf-core/holodeck/mutate | Process | simulation vcf mutations variants benchmarking | Generate a VCF of random mutations from a reference genome with holodeck |
| nf-core/holodeck/simulate | Process | simulation fastq reads sequencing benchmarking | Simulate sequencing reads from a reference genome with holodeck |
| nf-core/rtgtools/bndeval | Process | benchmarking vcf rtg-tools bnd-eval structural-variants | The bndeval tool of RTG tools. It is used to evaluate called BND type of variants for agreement with a BND baseline variant set |
| nf-core/rtgtools/cnveval | Process | benchmarking vcf rtg-tools cnv-eval copy-number-variants | The cnveval tool of RTG tools. It is used to evaluate called CNV regions for agreement with a baseline CNV set. |
| nf-core/rtgtools/vcfeval | Process | benchmarking vcf rtg-tools | The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set |
| 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/wittyer | Process | structural-variants benchmarking vcf | A large variant benchmarking tool analogous to hap.py for small variants. |