Nextflow Modules
Showing module(s) with keyword "variant"
| Module | Keywords | Description |
|---|---|---|
| nf-core/clair3 | germline variant Indel SNV | Clair3 is a germline small variant caller for long-reads |
| nf-core/graphtyper/genotype | variant vcf bam cram pangenome | Tools for population-scale genotyping using pangenome graphs. |
| nf-core/graphtyper/vcfconcatenate | combine concatenate variant vcf | Tools for population-scale genotyping using pangenome graphs. |
| nf-core/igvreports | vcf variant genomics | A Python application to generate self-contained HTML reports for variant review and other genomic applications |
| nf-core/jvarkit/vcffilterjdk | vcf bcf filter variant java script | Filtering VCF with dynamically-compiled java expressions |
| nf-core/nextclade/datasetget | nextclade variant consensus | Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation) |
| nf-core/nextclade/run | nextclade variant consensus | SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation) |
| nf-core/octopusv/correct | structural variant sv svcf normalize | Standardize a caller VCF into OctopuSV SVCF format. |
| nf-core/parabricks/deepvariant | variant deep variant vcf haplotypecaller germline | NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating deepvariant. |
| nf-core/parabricks/haplotypecaller | variant vcf haplotypecaller germline | NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating GATK haplotypecaller. |
| nf-core/parabricks/mutectcaller | variant vcf mutect2 mutect somatic | NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating GATK Mutect2. |
| nf-core/pbsv/call | variant pacbio genomics | pbsv/call - PacBio structural variant (SV) calling and analysis tools |
| nf-core/pbsv/discover | variant pacbio structural | pbsv - PacBio structural variant (SV) signature discovery tool |
| nf-core/platypus | variant call dna genetic | Platypus is a tool that efficiently and accurately calling genetic variants from next-generation DNA sequencing data |
| nf-core/plink/vcf | plink vcf variant call | Analyses variant calling files using plink |
| nf-core/snippy/run | variant fastq bacteria | Rapid haploid variant calling |
| nf-core/snpeff/download | annotation effect prediction snpeff variant vcf | Genetic variant annotation and functional effect prediction toolbox |
| nf-core/snpeff/snpeff | annotation effect prediction snpeff variant vcf | Genetic variant annotation and functional effect prediction toolbox |
| nf-core/snpsift/annmem | vcf annotation snpsift variant database | Annotate VCF files using pre-built SnpSift annMem databases. Enriches input VCF records by querying memory-optimized indexed dataframes for high-performance annotation. |
| nf-core/snpsift/annmemcreate | vcf annotation snpsift variant database | Create memory-optimized SnpSift vardb databases from VCF files for use with SnpSift annMem annotation. Converts VCF files (e.g. ClinVar, dbSNP, Cosmic) into indexed dataframes for fast lookup. |