Nextflow Modules
Showing module(s) with keyword "5mC"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_methyldackel | Workflow | 3-letter genome methylation 5mC methylseq bisulphite bisulfite bam | Performs methylation quantification based on negative readout of C to T conversion of 3-letter genome alignments using Methyldackel. |
| nf-core/bismark/align | Process | bismark 3-letter genome map methylation 5mC methylseq bisulphite bisulfite bam | Performs alignment of BS-Seq reads using bismark |
| nf-core/bismark/coverage2cytosine | Process | bismark consensus map methylation 5mC methylseq bisulphite bisulfite bam bedGraph | Relates methylation calls back to genomic cytosine contexts. |
| nf-core/bismark/deduplicate | Process | bismark 3-letter genome map methylation 5mC methylseq bisulphite bisulfite bam | Removes alignments to the same position in the genome from the Bismark mapping output. |
| nf-core/bismark/genomepreparation | Process | bismark 3-letter genome index methylation 5mC methylseq bisulphite bisulfite fasta | Converts a specified reference genome into two different bisulfite converted versions and indexes them for alignments. |
| nf-core/bismark/methylationextractor | Process | bismark consensus map methylation 5mC methylseq bisulphite bisulfite bam bedGraph | Extracts methylation information for individual cytosines from alignments. |
| nf-core/bismark/report | Process | bismark qc methylation 5mC methylseq bisulphite bisulfite report | Collects bismark alignment reports |
| nf-core/bismark/summary | Process | bismark qc methylation 5mC methylseq bisulphite bisulfite report summary | Uses Bismark report files of several samples in a run folder to generate a graphical summary HTML report. |
| nf-core/bwameth/align | Process | bwameth alignment 3-letter genome map methylation 5mC methylseq bisulphite bisulfite fastq bam | Performs alignment of BS-Seq reads using bwameth |
| nf-core/fastq_align_dedup_bismark | Workflow | bismark 3-letter genome map methylation 5mC methylseq bisulphite bisulfite bam | Align BS-Seq reads to a reference genome using bismark, deduplicate and sort |
| nf-core/fastq_align_dedup_bwamem | Workflow | bwamem alignment map 5mC methylseq DNA fastq bam | Performs alignment of DNA or TAPS-treated reads using bwamem or parabricks/fq2bam, sort and deduplicate |
| nf-core/fastq_align_dedup_bwameth | Workflow | bwameth alignment 3-letter genome map methylation 5mC methylseq bisulphite bisulfite fastq bam | Performs alignment of BS-Seq reads using bwameth or parabricks/fq2bammeth, sort and deduplicate |
| nf-core/methurator/gtestimator | Process | rrbs BS-seq methylation 5mC methylseq bisulphite bam | Run estimator for DNA methylation sequencing saturation. |
| nf-core/methurator/plot | Process | rrbs BS-seq methylation 5mC methylseq bisulphite bisulfite bam | Plots results produced by methurator gtestimator. |
| nf-core/methyldackel/extract | Process | methylation 5mC methylseq bisulphite bisulfite consensus bedGraph bam cram | Extracts per-base methylation metrics from alignments |
| nf-core/methyldackel/mbias | Process | methylation 5mC methylseq bisulphite bisulfite methylation bias mbias qc bam cram | Generates methylation bias plots from alignments |