Nextflow Modules
Showing module(s) with keyword "annotation"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/agat/spfilterbyorfsize | Process | 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 | Process | 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 | Process | genomics SINE annotation plant | Accelerating de novo SINE annotation in plant and animal genomes |
| nf-core/annotsv/annotsv | Process | annotation structural variants vcf bed tsv | Annotation and Ranking of Structural Variation |
| nf-core/annotsv/installannotations | Process | annotation download installation structural variants | Install the AnnotSV annotations |
| nf-core/atlasgeneannotationmanipulation/gtf2featureannotation | Process | gtf gene annotation | Generate tables of feature metadata from GTF files |
| nf-core/bakta/bakta | Process | annotation fasta bacteria | Annotation of bacterial genomes (isolates, MAGs) and plasmids |
| nf-core/bakta/baktadbdownload | Process | bakta annotation fasta bacteria database download | Downloads BAKTA database from Zenodo |
| nf-core/bcftools/csq | Process | annotation gff gff3 protein functional vcf bcf bcftools | bcftools Haplotype-aware consequence caller |
| nf-core/braker3 | Process | genome annotation braker gff gtf | Gene prediction in novel genomes using RNA-seq and protein homology information |
| nf-core/busco/generateplot | Process | genome fasta annotation busco transcriptome quality control | BUSCO plot generation tool |
| nf-core/busco/plot | Process | genome fasta annotation busco transcriptome quality control | BUSCO summary plot generation using the built-in 'busco --plot' command |
| nf-core/caalm/caalm | Process | 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/cache_download_ensemblvep_snpeff | Workflow | ensemblvep snpeff download annotation cache | downlad annotation cache for snpeff and ensemblvep |
| nf-core/caddsv/run | Process | caddsv structural variants deleteriousness annotation scoring | Score structural variants with CADD-SV. |
| nf-core/custom/addmostsevereconsequence | Process | annotation vep consequence vcf | Annotate a VEP annotated VCF with the most severe consequence field |
| nf-core/custom/addmostseverepli | Process | annotation vep pli |