Nextflow Modules
Showing module(s) with keyword "mapping"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/arcane/express | Process | single-cell rnaseq quantification mapping counts transcriptomics | Runs barcode correction, mapping, and UMI resolution in one go for single-cell RNA-seq quantification with Arcane |
| nf-core/circularmapper/circulargenerator | Process | bwa circular mapping genomics | A method to improve mappings on circular genomes, using the BWA mapper. |
| nf-core/coptr/estimate | Process | coptr mapping ptr | Calculates peak-to-through ratio (PTR) from metagenomic sequence data |
| nf-core/coptr/extract | Process | coptr mapping ptr | Computes the coverage map along the reference genome |
| nf-core/coptr/map | Process | coptr mapping ptr | Maps the reads to the reference database |
| nf-core/coptr/merge | Process | coptr mapping merging ptr | Merge reads that were mapped to multiple indices |
| nf-core/coverm/contig | Process | mapping genomics metagenomics coverage | Map reads to contigs and estimate coverage |
| nf-core/coverm/genome | Process | mapping genomics metagenomics coverage | Calculate read coverage per-genome |
| nf-core/mapad/map | Process | mapad ancient dna adna damage deamination miscoding lesions c to t palaeogenomics archaeogenomics palaeogenetics archaeogenetics short-read align aligner alignment map mapper mapping reference fasta fastq bam cram | Map short-reads to an indexed reference genome |
| nf-core/samtools/flagstat | Process | stats mapping counts bam sam cram | Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type |
| nf-core/samtools/idxstats | Process | stats mapping counts chromosome bam sam cram | Reports alignment summary statistics for a BAM/CRAM/SAM file |
| nf-core/slamdunk/all | Process | slamseq rna-seq mapping snp quantification | Complete SLAMseq analysis pipeline including read mapping, filtering, SNP calling, and quantification |
| nf-core/slamdunk/map | Process | slamseq rna-seq mapping | Slamdunk read mapping using NextGenMap’s SLAMSeq alignment settings. |
| nf-core/sortmerna | Process | filtering mapping clustering rRNA ribosomal RNA | Local sequence alignment tool for filtering, mapping and clustering. |
| nf-core/sourmash/index | Process | signatures sourmash genomics metagenomics mapping kmer | Create a database of sourmash signatures (a group of FracMinHash sketches) to be used as references. |