Nextflow Modules
Showing module(s) with keyword "bismark"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| 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/fasta_index_bismark_bwameth | Workflow | bismark bwameth prepare genome index | Generate index files from reference fasta for bismark and bwameth |
| nf-core/fasta_index_methylseq | Workflow | bismark bwameth bwamem prepare genome index | Generate index files from reference fasta for bismark, bwameth and bwamem aligners |
| 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 |