Nextflow Modules
Showing module(s) with keyword "ont"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/modkit/bedmethyltobigwig | Process | long-read ont methylation | Convert a bedMethyl file to bigWig format using modkit |
| nf-core/modkit/callmods | Process | methylation ont long-read | Call mods from a modbam, creates a new modbam with probabilities set to 100% if a base modification is called or 0% if called canonical |
| nf-core/modkit/dmr | Process | methylation ont long-read differential methylation | Compare regions between a pair of bedMethyl samples (e.g. two haplotypes, or tumor and normal) and report differentially methylated regions |
| nf-core/modkit/extractcalls | Process | modkit methylation extract calls read-level modbam nanopore ont | Produce a per-read per-position table of base modification **calls** (pass/fail/filtered, with the called base) from a modBAM using the same thresholding algorithm as `modkit pileup`. Complementary to `modkit extract full`, which emits raw probabilities: `extract calls` emits the thresholded categorical decision per site per read. |
| nf-core/modkit/extractfull | Process | modkit methylation extract read-level modbam nanopore ont | Transform the probabilities from the MM/ML tags in a modBAM into a tab-separated per-read-per-position table. Emits one row for every modified-base probability call in every read — useful for downstream custom filtering, plotting, and ML training. Optionally BGZF-compressed via `--bgzf` in `ext.args`. |
| nf-core/modkit/pileup | Process | methylation ont long-read | A bioinformatics tool for working with modified bases |
| nf-core/modkit/repair | Process | methylation ont long-read | Repair the MM/ML tags on trimmed or hard-clipped ONT reads using untrimmed ONT reads. |
| nf-core/modkit/validate | Process | modkit methylation validate nanopore ont modbam ground-truth benchmark | Validate base modification calls in one or more mod-BAMs against a matched ground-truth BED file containing the expected modification state at reference positions. Reports per-sample and combined confusion-matrix style statistics (accuracy, filtered calls, probability distribution) as a tab-separated machine-parseable table. |
| nf-core/polypolish/polish | Process | assembly polishing genome polishing ont | Polishing genome assemblies with short reads. |
| nf-core/ultra/align | Process | uLTRA align minimap2 long_read isoseq ont | uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Map reads on genome |
| nf-core/ultra/index | Process | uLTRA index minimap2 long_read isoseq ont | uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Index gtf file for reads alignment |
| nf-core/ultra/pipeline | Process | uLTRA index minimap2 long_read isoseq ont | uLTRA aligner - A wrapper around minimap2 to improve small exon detection |