Nextflow Modules
Showing module(s) with keyword "snp"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_ngscheckmate | Workflow | ngscheckmate qc bam snp | Take a set of bam files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs. |
| nf-core/eigenstratdatabasetools/eigenstratsnpcoverage | Process | coverage eigenstrat eigenstratdatabasetools snp snps | Provide the SNP coverage of each individual in an eigenstrat formatted dataset. |
| nf-core/fastq_ngscheckmate | Workflow | ngscheckmate qc fastq snp | Take a set of fastq files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs. |
| nf-core/ngscheckmate/fastq | Process | ngscheckmate matching snp qc | Determining whether sequencing data comes from the same individual by using SNP matching. This module generates vaf files for individual fastq file(s), ready for the vafncm module. |
| nf-core/ngscheckmate/ncm | Process | ngscheckmate matching snp | Determining whether sequencing data comes from the same individual by using SNP matching. Designed for humans on vcf or bam files. |
| nf-core/ngscheckmate/patterngenerator | Process | ngscheckmate matching snp qc | Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions. |
| nf-core/ngscheckmate/vafncm | Process | ngscheckmate matching snp qc | Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions. |
| nf-core/slamdunk/all | Process | slamseq rna-seq mapping snp quantification | Complete SLAMseq analysis pipeline including read mapping, filtering, SNP calling, and quantification |
| nf-core/snpclustering | Workflow | snp clustering pca plink2 beagle imputation population genetics | Subworkflow for SNP clustering. Takes genotyped VCF files, imputes missing genotypes with BEAGLE5, converts to PLINK2 pgen format, performs PCA,then runs PCA-based clustering, cluster metrics, and cluster visualization. |
| nf-core/snpdists | Process | snp dist distance matrix | Pairwise SNP distance matrix from a FASTA sequence alignment |