Nextflow Modules
Showing module(s) with keyword "prediction"
| Module | Keywords | Description |
|---|---|---|
| nf-core/amplify/predict | antimicrobial peptides AMPs prediction model | AMPlify is an attentive deep learning model for antimicrobial peptide prediction. |
| nf-core/deeparg/downloaddata | download database deeparg antimicrobial resistance genes deep learning prediction | A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes |
| nf-core/deeparg/predict | deeparg antimicrobial resistance antimicrobial resistance genes arg deep learning prediction contigs metagenomes | A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes |
| nf-core/deepmased/predict | metagenomics assembly quality control error detection deep learning prediction | DeepMAsED predict subcommand: runs the pre-trained deep learning model on feature tables produced by DeepMAsED features to predict per-contig assembly error scores. |
| nf-core/fungtion/downloadmodels | fungal effector protein prediction language model deep learning model download | Downloads the pretrained ESM-1b weights (esm1b_t33_650M_UR50S.pt) that fungtion uses for fungal effector prediction into a local models/ directory via `fungtion setup-models`. The downloaded directory is used as input to the FUNGTION_FUNGTION prediction module. |
| 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/islandpath | genomes genomic islands prediction | Genomic island prediction in bacterial and archaeal genomes |
| nf-core/pyrodigal | sort annotation prediction prokaryote | Pyrodigal is a Python module that provides bindings to Prodigal, a fast, reliable protein-coding gene prediction for prokaryotic genomes. |
| nf-core/rpbp/selectfinalpredictionset | rpbp orf bayes prediction riboseq | Produce the final filtered set of predicted translated ORFs from the per-ORF Bayes factor table. Applies the standard Rp-Bp prediction rules: a minimum Bayes-factor cutoff (favouring translated over untranslated), a minimum ORF length, and overlap resolution so that among overlapping candidates only the highest-scoring representative is kept. Emits three files describing the same prediction set: a BED of ORF genomic coordinates plus score, a FASTA of ORF DNA sequences (extracted from the genome FASTA), and a FASTA of the corresponding translated protein sequences. This is the terminal step of the Rp-Bp per-sample chain. |
| nf-core/s4pred/runmodel | protein secondary structure prediction | Prediction of a protein's secondary structure from its amino acid sequence |
| nf-core/traitar/run | phenotype prediction microbial traits genomics protein families | Traitar3 - predict microbial phenotypes from genomic sequences using protein families |
| nf-core/tsebra | genomics transcript selector gene prediction evidence | Transcript Selector for BRAKER TSEBRA combines gene predictions by selecting transcripts based on their extrisic evidence support |