Nextflow Modules
Showing module(s) with keyword "cluster"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/cdhit/cdhit | Process | cluster protein alignment fasta | Cluster protein sequences using sequence similarity |
| nf-core/cdhit/cdhitest | Process | cluster nucleotide alignment fasta | Cluster nucleotide sequences using sequence similarity |
| nf-core/clusty | Process | cluster network contig scaffold alignment protein | Clusty is a tool for large-scale clustering using sparse distance matrices, suitable for datasets with millions of objects. |
| nf-core/fasta_vclust_prefilter_align_cluster | Workflow | fasta vclust cluster prefilter align | Subworkflow that runs a three-stage VCLUST pipeline: 1) create a prefilter of candidate sequence pairs with `vclust prefilter`, 2) compute pairwise alignments and similarity metrics with `vclust align`, and 3) generate threshold-based clusters with `vclust cluster`. |
| nf-core/galah | Process | genomics cluster genome metagenomics | Cluster genome FASTA files by average nucleotide identity |
| nf-core/isoseq/cluster | Process | cluster HiFi isoseq Pacbio | IsoSeq - Cluster - Cluster trimmed consensus sequences |
| nf-core/isoseq/cluster2 | Process | cluster HiFi isoseq Pacbio | IsoSeq - Cluster2 - Cluster full-length non-chimeric reads into transcripts |
| nf-core/mmseqs_fasta_cluster | Workflow | fasta sequences cluster linclust mmseqs | Subworkflow that generates a clustering TSV file from a set of amino acid sequence within a FASTA file. |
| nf-core/mobsuite/recon | Process | bacteria plasmid cluster | A tool to reconstruct plasmids in bacterial assemblies |
| nf-core/paraclu | Process | sort cluster bed | Paraclu finds clusters in data attached to sequences. |
| nf-core/rattle/cluster | Process | transcriptomes cluster nanopore | Reference-free reconstruction and quantification of transcriptomes from long-read sequencing |
| nf-core/seqcluster/collapse | Process | smrnaseq cluster mirna | Seqcluster collapse reduces computational complexity by collapsing identical sequences in a FASTQ file. |
| nf-core/trycycler/cluster | Process | cluster alignment fastq fasta genomics | Cluster contigs from multiple assemblies by similarity |
| nf-core/vclust/align | Process | cluster virus filter contig scaffold phage | The align command performs pairwise sequence alignments of viral genomes and provides similarity measures like ANI and coverage (alignment fraction) |
| nf-core/vclust/cluster | Process | cluster virus filter contig scaffold phage | Vclust cluster performs threshold-based clustering by assigning a genome sequence to a cluster if its similarity (e.g., ANI) to the cluster meets or exceeds a user-defined threshold. |
| nf-core/vclust/prefilter | Process | cluster virus filter contig scaffold phage | The prefilter command creates a pre-alignment filter that reduces the number of genome pairs to be aligned by filtering out dissimilar sequences before the alignment step. |