Nextflow Modules
Showing module(s) with keyword "annotation"
| Module | Keywords | Description |
|---|---|---|
| nf-core/agat/spfilterbyorfsize | genomics GFF/GTF filter annotation | The script reads a gff annotation file, and create two output files, one contains the gene models with ORF passing the test, the other contains the rest. By default the test is "> 100" that means all gene models that have ORF longer than 100 Amino acids, will pass the test. |
| nf-core/agat/spflagshortintrons | genomics gtf gff intron short annotation | The script flags the short introns with the attribute <pseudo>. Is is usefull to avoid ERROR when submiting the data to EBI. (Typical EBI error message: ********ERROR: Intron usually expected to be at least 10 nt long. Please check the accuracy) |
| nf-core/annosine | genomics SINE annotation plant | Accelerating de novo SINE annotation in plant and animal genomes |
| nf-core/annotsv/annotsv | annotation structural variants vcf bed tsv | Annotation and Ranking of Structural Variation |
| nf-core/annotsv/installannotations | annotation download installation structural variants | Install the AnnotSV annotations |
| nf-core/atlasgeneannotationmanipulation/gtf2featureannotation | gtf gene annotation | Generate tables of feature metadata from GTF files |
| nf-core/bakta/bakta | annotation fasta bacteria | Annotation of bacterial genomes (isolates, MAGs) and plasmids |
| nf-core/bakta/baktadbdownload | bakta annotation fasta bacteria database download | Downloads BAKTA database from Zenodo |
| nf-core/bcftools/csq | annotation gff gff3 protein functional vcf bcf bcftools | bcftools Haplotype-aware consequence caller |
| nf-core/braker3 | genome annotation braker gff gtf | Gene prediction in novel genomes using RNA-seq and protein homology information |
| nf-core/busco/generateplot | genome fasta annotation busco transcriptome quality control | BUSCO plot generation tool |
| 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/custom/addmostsevereconsequence | annotation vep consequence vcf | Annotate a VEP annotated VCF with the most severe consequence field |
| nf-core/custom/addmostseverepli | annotation vep pli vcf | Annotate a VEP annotated VCF with the most severe pLi field |
| nf-core/ea-utils/gtf2bed | gtf gff bed bed12 annotation conversion | Convert a GTF/GFF annotation file to BED12 format |
| nf-core/eggnogmapper | annotation functional annotation orthology genomics eggnog | Fast genome-wide functional annotation through orthology assignment. |
| nf-core/ensemblvep/download | annotation cache download | Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through `task.ext.args`. |
| nf-core/ensemblvep/filtervep | annotation vcf tab filter | Filter variants based on Ensembl Variant Effect Predictor (VEP) annotations. |
| nf-core/ensemblvep/vep | annotation vcf json |