Nextflow Modules
Showing module(s) with keyword "nanopore"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/artic/aligntrim | Process | artic primer trimming amplicon genomics sequencing nanopore illumina | Standalone version of fieldbioinformatics aligntrim. Soft clips amplicon scheme primer sites in BAM/SAM files. |
| nf-core/canu | Process | Assembly pacbio hifi nanopore | Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. |
| nf-core/chopper | Process | filter trimming fastq nanopore qc chopper pigz multi-tool | Filter and trim long read data. |
| nf-core/dragonflye | Process | bacterial assembly nanopore | Assemble bacterial isolate genomes from Nanopore reads |
| nf-core/emu/abundance | Process | metagenomics 16S nanopore | A taxonomic profiler for metagenomic 16S data optimized for error prone long reads. |
| nf-core/filtlong | Process | nanopore quality control QC filtering long reads short reads | Filtlong filters long reads based on quality measures or short read data. |
| nf-core/gstama/collapse | Process | tama_collapse.py isoseq nanopore long-read transcriptome gene model TAMA | Collapse redundant transcript models in Iso-Seq data. |
| nf-core/gstama/merge | Process | gstama gstama/merge long-read isoseq nanopore tama trancriptome annotation | Merge multiple transcriptomes while maintaining source information. |
| nf-core/hypo | Process | assembly polishing nanopore illumina | Assembly polisher using short (and long) reads |
| nf-core/medaka | Process | assembly polishing nanopore | A tool to create consensus sequences and variant calls from nanopore sequencing data |
| nf-core/melon | Process | profile metagenomics melon classification long reads nanopore | Performs taxonomic profiling of long metagenomic reads against the melon database |
| nf-core/miniasm | Process | assembly pacbio nanopore | A very fast OLC-based de novo assembler for noisy long reads |
| 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/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/myloasm | Process |