Nextflow Modules
Showing module(s) with keyword "consensus"
| 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/aardvark/merge | Process | variant calling vcf comparison consensus merging | A tool to evaluate and merge multiple variant calls into a consensus VCF. |
| nf-core/autocycler/combine | Process | autocycler genome-assembly consensus long-read | Merge resolved cluster assemblies into final consensus outputs with Autocycler. |
| nf-core/bcftools/consensus | Process | variant calling consensus VCF | Compresses VCF files |
| nf-core/bismark/coverage2cytosine | Process | bismark consensus map methylation 5mC methylseq bisulphite bisulfite bam bedGraph | Relates methylation calls back to genomic cytosine contexts. |
| nf-core/bismark/methylationextractor | Process | bismark consensus map methylation 5mC methylseq bisulphite bisulfite bam bedGraph | Extracts methylation information for individual cytosines from alignments. |
| nf-core/emboss/cons | Process | emboss consensus fasta multiple sequence alignment MSA | cons calculates a consensus sequence from a multiple sequence alignment. To obtain the consensus, the sequence weights and a scoring matrix are used to calculate a score for each amino acid residue or nucleotide at each position in the alignment. |
| nf-core/fasta_consensus_autocycler | Workflow | autocycler consensus assembly fasta | Generate consensus assemblies and assembly graphs from grouped contig FASTA files using autocycler |
| nf-core/fgbio/filterconsensusreads | Process | fgbio filter consensus umi duplexumi | Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads. |
| nf-core/fgumi/codec | Process | UMIs consensus codec bam duplex | Call CODEC consensus reads from a UMI-grouped BAM with fgumi |
| nf-core/fgumi/duplex | Process | umi duplex consensus bam | Calls duplex consensus sequences from reads generated from the same double-stranded source molecule. This is a high-performance replacement for fgbio CallDuplexConsensusReads. |
| nf-core/fgumi/filter | Process | umi filter consensus bam | Filters consensus reads generated by simplex or duplex consensus calling. This is a high-performance replacement for fgbio FilterConsensusReads. |
| nf-core/fgumi/simplex | Process | umi consensus simplex bam | Calls simplex consensus sequences from reads with the same unique molecular tag. This is a high-performance replacement for fgbio CallMolecularConsensusReads. |
| nf-core/ivar/consensus | Process | amplicon sequencing consensus fasta | Generate a consensus sequence from a BAM file using iVar |
| nf-core/methyldackel/extract | Process | methylation 5mC methylseq bisulphite bisulfite consensus bedGraph bam cram | Extracts per-base methylation metrics from alignments |
| nf-core/nextclade/datasetget | Process | nextclade variant consensus | Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation) |
| nf-core/nextclade/run | Process |