Nextflow Modules
Showing module(s) with keyword "bisulfite"
| Module | Keywords | Description |
|---|---|---|
| nf-core/biscuit/pileup | bisulfite DNA methylation pileup variant calling WGBS scWGBS bam vcf | Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants |
| 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/bwameth/index | bwameth 3-letter genome index methylseq bisulphite bisulfite fasta | Performs indexing of c2t converted reference genome |
| 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 | Build HISAT-3N index for nucleotide conversion sequencing alignment |
| nf-core/holodeck/methylate | simulation vcf methylation bisulfite benchmarking | Generate a methylation-annotated VCF from a reference genome with holodeck |
| nf-core/methurator/plot | rrbs BS-seq methylation 5mC methylseq bisulphite bisulfite bam | Plots results produced by methurator gtestimator. |
| nf-core/methyldackel/extract | methylation 5mC methylseq bisulphite bisulfite consensus bedGraph bam cram | Extracts per-base methylation metrics from alignments |
| nf-core/methyldackel/mbias | methylation 5mC methylseq bisulphite bisulfite methylation bias mbias qc bam cram | Generates methylation bias plots from alignments |
| nf-core/methylsieve | methylation bisulfite em-seq unconverted bam qc | Filter/tag unconverted reads in methylation sequencing with methylsieve; for maximum throughput it can also run inline in the alignment pipe (aligner | methylsieve | sort) rather than as a standalone step |
| nf-core/rastair/call | methylation rastair C->T conversion bisulphite bisulfite bam mCtoT | Assess positive C->T conversion as a readout for methylation on a genome-wide basis |
| nf-core/rastair/mbias | methylation rastair C->T conversion bisulphite bisulfite bam mCtoT mbias methylation bias | Assess C->T conversion as a readout for methylation on a per-read-position basis. |
| nf-core/rastair/mbiasparser | methylation rastair C->T conversion bisulphite bisulfite bam mCtoT mbias methylation bias mbiasparser cutoff | Parses Rastair mbias output to assess the ideal cutoff for read trimming and reports the values. |