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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/methyldackel/extract methylation 5mC