Nextflow Modules
Showing module(s) with keyword "map"
| Module | Keywords | Description |
|---|---|---|
| nf-core/bbmap/align | align map fasta fastq genome reference | Align short or PacBio reads to a reference genome using BBMap |
| nf-core/bbmap/bbsplit | align map fastq genome reference | Split sequencing reads by mapping them to multiple references simultaneously |
| nf-core/bbmap/index | map index fasta | Creates an index from a fasta file, ready to be used by bbmap.sh in mapping mode. |
| nf-core/bedtools/map | bed vcf gff map bedtools | Allows one to screen for overlaps between two sets of genomic features. |
| 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/methylationextractor | bismark consensus map methylation 5mC methylseq bisulphite bisulfite bam bedGraph | Extracts methylation information for individual cytosines from alignments. |
| nf-core/bowtie2/align | align map fasta fastq genome reference | Align reads to a reference genome using bowtie2 |
| nf-core/bowtie/align | align map fastq fasta genome reference | Align reads to a reference genome using bowtie |
| nf-core/bwa/aln | bwa aln short-read align reference fasta map fastq | Find SA coordinates of the input reads for bwa short-read mapping |
| nf-core/bwa/mem | mem bwa alignment map fastq bam sam | Performs fastq alignment to a fasta reference using BWA |
| nf-core/bwamem2/mem | mem bwa alignment map fastq bam sam | Performs fastq alignment to a fasta reference using BWA |
| nf-core/bwameme/mem | mem bwa bwamem2 bwameme alignment map fastq bam sam cram | Performs fastq alignment to a fasta reference using BWA-MEME |
| nf-core/bwameth/align | bwameth alignment 3-letter genome map methylation 5mC |