Nextflow Modules
Showing module(s) with keyword "population genetics"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/admixture | Process | ancestry population genetics admixture reference panels gwas | ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study). |
| nf-core/angsd/contamination | Process | angsd population genetics nuclear contamination estimate | A tool to estimate nuclear contamination in males based on heterozygosity in the female chromosome. |
| nf-core/angsd/docounts | Process | angsd population genetics allele counts doCounts | Calculates base frequency statistics across reference positions from BAM. |
| nf-core/atlas/call | Process | atlas variant calling vcf population genetics | generate VCF file from a BAM file using various calling methods |
| nf-core/pcaone | Process | pca population genetics dimensionality reduction svd genotype | Fast, accurate and memory-efficient PCA on large-scale genotype or single-cell data |
| 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/vsearch/dereplicate | Process | vsearch/dereplicate vsearch dereplicate amplicon sequences metagenomics genomics population genetics | Merge strictly identical sequences contained in filename. Identical sequences are defined as having the same length and the same string of nucleotides (case insensitive, T and U are considered the same). |
| nf-core/vsearch/fastqfilter | Process | vsearch/fastqfilter vsearch fastqfilter amplicon sequences metagenomics genomics population genetics | Performs quality filtering and / or conversion of a FASTQ file to FASTA format. |
| nf-core/vsearch/sort | Process | vsearch/sort vsearch sort amplicon sequences metagenomics genomics population genetics | Sort fasta entries by decreasing abundance (--sortbysize) or sequence length (--sortbylength). |