Nextflow Modules
Showing module(s) with keyword "WGS"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/canvas/germline | Process | CNV copy number variants germline WGS canvas | Calls germline copy number variants (CNVs) from whole genome sequencing data using Illumina Canvas in SmallPedigree-WGS mode. Although named SmallPedigree-WGS, this mode is recommended for single germline samples as well as small pedigrees. The module accepts aligned reads (BAM), germline SNV calls, and sex-specific ploidy information, and outputs a VCF with copy number status across the genome together with a coverage-and-variant-frequency file used for downstream segmentation. |
| nf-core/chewbbaca/allelecall | Process | cgMLST WGS genomics | Determine the allelic profiles of a genome using a pre-defined schema |
| nf-core/chewbbaca/createschema | Process | cgMLST WGS genomics | Create a schema to determine the allelic profiles of a genome |
| nf-core/cnaqc | Process | WGS copy number quality control | Quality control of copy number data from bulk WGS assays |
| nf-core/pyclonevi | Process | clonal population WGS subclonal deconvolution copy number alterations somatic mutations | PyClone-VI is a software for inferring the clonal population structure of cancers by using variant allele frequencies and copy number data of single or multiple samples. |