Nextflow Modules
Showing module(s) with keyword "taxonomy"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bbmap/sendsketch | Process | taxonomy classification sketch query fastq fasta | Compares query sketches to reference sketches hosted on a remote server via the Internet. |
| nf-core/custom/resolvetaxonomy | Process | taxonomy fasta phylogenetics | Resolve the taxonomy for a set of sequences: use an explicit taxonomy file if one is given (warning, not silently ignoring, if the sequences also carry embedded taxonomy text); otherwise derive taxonomy from each sequence's own FASTA header, GTDB-style (`>id taxonomy;string`). Headers are always stripped down to a bare id in the output sequences, regardless of which taxonomy source was used. When taxonomy_required is false, records with neither source are dropped from the resolved taxonomy (with a warning) instead of failing the run. |
| nf-core/fasta_classify_catpack | Workflow | metagenomics taxonomy classification bins MAGs contigs CAT BAT | Taxonomic classification of binned MAGs and contigs using CAT/BAT (CAT_pack). |
| nf-core/ganon/buildcustom | Process | ganon metagenomics profiling taxonomy k-mer database | Build ganon database using custom reference sequences. |
| nf-core/ganon/classify | Process | ganon metagenomics profiling taxonomy k-mer classification classify | Classify FASTQ files against ganon database |
| nf-core/ganon/report | Process | ganon metagenomics profiling taxonomy k-mer classification report | Generate a ganon report file from the output of ganon classify |
| nf-core/ganon/table | Process | ganon metagenomics profiling taxonomy k-mer classification report table | Generate a multi-sample report file from the output of ganon report runs |
| nf-core/gappa/examineassign | Process | phylogeny phylogenetic placement classification taxonomy | assigns taxonomy to query sequences in phylogenetic placement output |
| nf-core/grimer | Process | metagenomics contamination visualisation taxonomy viromics microbiome dashboard | Generates an interactive HTML dashboard integrating taxonomy, annotation, and metadata to detect contamination in metagenomic and amplicon sequencing datasets. GRIMER is independent of quantification methods and directly analyses contingency tables. |
| nf-core/gtdbtk/gtdbtoncbimajorityvote | Process | gtdb taxonomy ncbi taxonomy taxonomic classification conversion taxonomy classification genome taxonomy database bacteria archaea | Converts the output classifications of GTDB-TK from GTDB taxonomy to NCBI taxonomy |
| nf-core/kaiju/kaiju2krona | Process | taxonomy visualisation krona chart metagenomics | Convert Kaiju's tab-separated output file into a tab-separated text file which can be imported into Krona. |
| nf-core/krona/kronadb | Process | database taxonomy krona | KronaTools Update Taxonomy downloads a taxonomy database |
| nf-core/krona/ktimportkrona | Process | plot taxonomy interactive html visualisation krona chart | Collect multiple krona reports into a single html file |
| nf-core/krona/ktimporttaxonomy | Process | plot taxonomy interactive html visualisation krona chart | KronaTools Import Taxonomy imports taxonomy classifications and produces an interactive Krona plot. |
| nf-core/krona/ktimporttext | Process | plot |