Nextflow Modules
Showing module(s) with keyword "consensus"
| Module | Keywords | Description |
|---|---|---|
| nf-core/autocycler/combine | autocycler genome-assembly consensus long-read | Merge resolved cluster assemblies into final consensus outputs with Autocycler. |
| nf-core/bcftools/consensus | variant calling consensus VCF | Compresses VCF files |
| nf-core/bismark/coverage2cytosine | bismark consensus map methylation 5mC methylseq bisulphite bisulfite bam bedGraph | Relates methylation calls back to genomic cytosine contexts. |
| nf-core/bismark/methylationextractor | bismark consensus map methylation 5mC methylseq bisulphite bisulfite bam bedGraph | Extracts methylation information for individual cytosines from alignments. |
| nf-core/emboss/cons | 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/fgbio/filterconsensusreads | fgbio filter consensus umi duplexumi | Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads. |
| nf-core/ivar/consensus | amplicon sequencing consensus fasta | Generate a consensus sequence from a BAM file using iVar |
| nf-core/methyldackel/extract | methylation 5mC methylseq bisulphite bisulfite consensus bedGraph bam cram | Extracts per-base methylation metrics from alignments |
| 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/ragtag/patch | assembly consensus ragtag patch | Homology-based assembly patching: Make continuous joins and fill gaps in 'target.fa' using sequences from 'query.fa' |
| nf-core/samtools/consensus | consensus bam fastq fasta pileup | Produces a consensus FASTA/FASTQ/PILEUP |
| nf-core/topas/gencons | consensus fasta ancient DNA | Create fasta consensus with TOPAS toolkit with options to penalize substitutions for typical DNA damage present in ancient DNA |
| nf-core/viralconsensus | virus genomics consensus bam fasta | Fast and memory-efficient viral consensus genome sequence generation from read alignments |