Nextflow Modules
Showing module(s) with keyword "classification"
| Module | Keywords | Description |
|---|---|---|
| nf-core/bbmap/sendsketch | taxonomy classification sketch query fastq fasta | Compares query sketches to reference sketches hosted on a remote server via the Internet. |
| nf-core/caalm/caalm | cazyme annotation protein language model deep learning classification | Annotates carbohydrate-active enzyme (CAZyme) families from protein sequences using protein language model (ESM) embeddings and FAISS-based nearest-neighbour search. Performs three-level hierarchical classification: binary CAZyme detection (Level 0), CAZy class assignment (Level 1), and CAZy family assignment (Level 2). |
| nf-core/catpack/addnames | taxonomic classification classification long reads mags assembly | Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins). |
| nf-core/catpack/bins | taxonomic classification classification long reads mags assembly | Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins). |
| nf-core/catpack/contigs | taxonomic classification classification long reads mags assembly | Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins). |
| nf-core/catpack/download | taxonomic classification classification database download | Downloads the required files for either Nr or GTDB for building into a CAT database |
| nf-core/catpack/reads | taxonomic classification classification long reads mags assembly abundance taxonomic composition | Taxonomic classification plus read-based abundance estimation from long DNA sequences and metagenome assembled genomes (e.g. contigs, MAGs / bins). |
| nf-core/catpack/summarise | taxonomic classification classification long reads mags assembly | Summarises results from CAT/BAT/RAT classification steps |
| nf-core/centrifuger/centrifuger | metagenomics classification centrifuger | Classification of sequencing reads using the Centrifuger tool. |
| nf-core/deeptmhmm | transmembrane protein classification | A Deep Learning Model for Transmembrane Topology Prediction and Classification |
| nf-core/fungtion/fungtion | fungal effector protein prediction language model deep learning svm classification | Predicts fungal effector proteins from protein FASTA sequences using ESM-1b protein language model embeddings and R-based SVM models. Optionally produces similarity-network and relationship-tree visualizations and an HTML report for predicted effectors. Requires the pretrained ESM-1b weights from FUNGTION_DOWNLOADMODELS as input. |
| nf-core/ganon/classify | ganon metagenomics profiling taxonomy k-mer classification classify | Classify FASTQ files against ganon database |
| nf-core/ganon/report | ganon metagenomics profiling taxonomy k-mer classification report | Generate a ganon report file from the output of ganon classify |
| nf-core/ganon/table | 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 | phylogeny phylogenetic placement classification taxonomy | assigns taxonomy to query sequences in phylogenetic placement output |
| nf-core/gtdbtk/classifywf | GTDB taxonomy taxonomic classification metagenomics classification genome taxonomy database bacteria archaea | GTDB-Tk is |