Nextflow Modules
Showing module(s) with keyword "bed"
| Module | Keywords | Description |
|---|---|---|
| nf-core/agat/convertbed2gff | genome bed gff conversion | Takes a bed12 file and converts to a GFF3 file |
| nf-core/agat/convertgff2bed | genome bed gff conversion | Takes a GFF3 file and converts to a bed12 file |
| nf-core/annotsv/annotsv | annotation structural variants vcf bed tsv | Annotation and Ranking of Structural Variation |
| nf-core/bamtools/convert | bamtools bamtools/convert bam convert bed fasta fastq json pileup sam yaml | BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. |
| nf-core/bedgovcf | bed vcf conversion variants | Convert a BED file to a VCF file according to a YAML config |
| nf-core/bedops/convert2bed | convert bed genomics | Convert BAM/GFF/GTF/GVF/PSL files to bed |
| nf-core/bedops/gtf2bed | gtf bed conversion | Convert gtf format to bed format |
| nf-core/bedtools/bamtobed | bam bed bedtools bamtobed converter | Converts a bam file to a bed12 file. |
| nf-core/bedtools/closest | bedtools closest bed vcf gff | For each feature in A, finds the closest feature (upstream or downstream) in B. |
| nf-core/bedtools/complement | bed gff vcf complement bedtools intervals | Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file. |
| nf-core/bedtools/coverage | bedtools coverage bam bed gff vcf histogram | computes both the depth and breadth of coverage of features in file B on the features in file A |
| nf-core/bedtools/flank | bed flankBed bedtools | Creates two new flanking intervals for each interval in a BED/GFF/VCF file. |
| nf-core/bedtools/genomecov | bed bam genomecov bedtools histogram | Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome. |
| nf-core/bedtools/getfasta | bed fasta getfasta | extract sequences in a FASTA file based on intervals defined in a feature file. |
| nf-core/bedtools/groupby | bed groupby bedtools | Groups features in a BED file by given column(s) and computes summary statistics for each group to another column. |
| nf-core/bedtools/intersect | bed intersect overlap | Allows one to screen for overlaps between two sets of genomic features. |
| nf-core/bedtools/jaccard | vcf gff bed jaccard intersection union statistics | Calculate Jaccard statistic b/w two feature files. |
| nf-core/bedtools/makewindows | bed windows fai chunking | Makes adjacent or sliding windows across a genome or BED file. |
| nf-core/bedtools/map | bed vcf gff map bedtools | Allows one to screen for overlaps between two sets of genomic features. |
| nf-core/bedtools/maskfasta | bed fasta maskfasta |