Nextflow Modules
Showing module(s) with keyword "long-read"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/autocycler/cluster | Process | autocycler genome-assembly clustering long-read | Cluster replicons in compressed assemblies with Autocycler. |
| nf-core/autocycler/combine | Process | autocycler genome-assembly consensus long-read | Merge resolved cluster assemblies into final consensus outputs with Autocycler. |
| nf-core/autocycler/compress | Process | autocycler genome-assembly compression long-read | Package candidate assemblies for clustering by Autocycler. |
| nf-core/autocycler/resolve | Process | autocycler genome-assembly graph-resolution long-read | Resolve trimmed assembly graphs into final contigs within Autocycler. |
| nf-core/autocycler/subsample | Process | autocycler subsampling long-read | Downsample long-read sequencing data to the requested coverage using Autocycler. |
| nf-core/autocycler/trim | Process | autocycler genome-assembly graph-trimming long-read | Trim cluster assembly graphs to remove unsupported segments prior to resolution. |
| nf-core/cramino | Process | quality assessment bam long-read genomics | Quality assessment of long-read bam files using cramino. |
| nf-core/debreak | Process | debreak structural variants long-read SV calling | Structural variant calling from long-read sequencing data using DeBreak |
| 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/gstama/polyacleanup | Process | gstama gstama/polyacleanup long-read isoseq tama trancriptome annotation | Helper script, remove remaining polyA sequences from Full Length Non Chimeric reads (Pacbio isoseq3) |
| nf-core/longphase/haplotag | Process | haplotag long-read genomics | LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms. |
| nf-core/longphase/phase | Process | phase long-read genomics | LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms. |
| 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/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/myloasm | Process | assembly |