Nextflow Modules
Showing module(s) with keyword "gtf"
| Module | Keywords | Description |
|---|---|---|
| nf-core/agat/convertspgff2gtf | genome gff gtf conversion | Converts a GFF/GTF file into a proper GTF file |
| nf-core/agat/convertspgff2tsv | genome gff gtf conversion tsv | Converts a GFF/GTF file into a TSV file |
| nf-core/agat/convertspgxf2gxf | genome gff gtf conversion | Fixes and standardizes GFF/GTF files and outputs a cleaned GFF/GTF file |
| nf-core/agat/spaddintrons | gtf gff introns | Add intron features to gtf/gff file without intron features. |
| 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/agat/spkeeplongestisoform | gff gtf filter isoform gene longest agat | Filters GFF records to keep only the longest isoform per gene |
| nf-core/agat/spstatistics | genome gff gtf statistics | Provides different type of statistics in text format from a GFF/GTF annotation file |
| nf-core/agat/sqstatbasic | genome gff gtf statistics | Provides basic statistics in text format from a GFF/GTF annotation file |
| nf-core/atlasgeneannotationmanipulation/gtf2featureannotation | gtf gene annotation | Generate tables of feature metadata from GTF files |
| nf-core/bedops/gtf2bed | gtf bed conversion | Convert gtf format to bed format |
| nf-core/braker3 | genome annotation braker gff gtf | Gene prediction in novel genomes using RNA-seq and protein homology information |
| nf-core/custom/catadditionalfasta | fasta gtf genomics | Custom module to Add a new fasta file to an old one and update an associated GTF |
| nf-core/custom/gtffilter | gtf fasta filter | Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file |
| nf-core/custom/tx2gene | gene gtf pseudoalignment rsem transcript | Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications. |
| nf-core/ea-utils/gtf2bed | gtf gff bed bed12 annotation conversion | Convert a GTF/GFF annotation file to BED12 format |
| nf-core/gffcompare | transcripts gtf merge compare | Compare, merge, annotate and estimate accuracy of generated gtf files |
| nf-core/gtfsort | sort genomics gtf | Sort GTF files in chr/pos/feature order |
| nf-core/hisat2/extractsplicesites | splicing gtf genome reference | Extracts splicing sites from a gtf files |
| nf-core/htseq/count | htseq count gtf annotation | count how many reads map to each feature |
| nf-core/icountmini/metagene | iCLIP gtf genomics | Plot a metagene of cross-link events/sites around various transcriptomic landmarks. |