Nextflow Modules
Showing module(s) with keyword "methylation"
| Module | Keywords | Description |
|---|---|---|
| nf-core/bismark/align | bismark 3-letter genome map methylation 5mC methylseq bisulphite bisulfite bam | Performs alignment of BS-Seq reads using bismark |
| nf-core/bismark/coverage2cytosine | bismark consensus map methylation 5mC methylseq bisulphite bisulfite bam bedGraph | Relates methylation calls back to genomic cytosine contexts. |
| nf-core/bismark/deduplicate | 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 | 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 | bismark consensus map methylation 5mC methylseq bisulphite bisulfite bam bedGraph | Extracts methylation information for individual cytosines from alignments. |
| nf-core/bismark/report | bismark qc methylation 5mC methylseq bisulphite bisulfite report | Collects bismark alignment reports |
| nf-core/bismark/summary | 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 | bwameth alignment 3-letter genome map methylation 5mC methylseq bisulphite bisulfite fastq bam | Performs alignment of BS-Seq reads using bwameth |
| nf-core/fibertoolsrs/addnucleosomes | methylation genomics bam m6A nucleosome fiberseq | Add nucleosomes positions and MSP position to ONT BAM files |
| nf-core/fibertoolsrs/extract | methylation genomics bam m6A fiberseq | Extract Fiber-seq information (such as m6A, CpG, nucleosomes, and MSPs) from BAM file into BED file |
| nf-core/fibertoolsrs/predictm6a | methylation genomics bam m6A nucleosome fiberseq | Predict m6A positions using HiFi kinetics data and encode the results in the MM and ML bam tags. Also adds nucleosome (nl, ns) and MTase sensitive patches (al, as) |
| nf-core/hisat3n/align | align bisulfite methylation nucleotide conversion SLAM-seq fastq genome | Align nucleotide conversion sequencing reads (e.g., bisulfite-seq, SLAM-seq) to a reference genome with HISAT-3N |
| nf-core/hisat3n/build | build index fasta genome reference bisulfite methylation |