Nextflow Modules
Showing module(s) with keyword "BAM"
| Module | Keywords | Description |
|---|---|---|
| nf-core/bamreadcount | BAM CRAM metrics genomics | bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads. |
| nf-core/biscuit/qc | biscuit DNA methylation WGBS scWGBS bisulfite sequencing index BAM quality control | Perform basic quality control on a BAM file generated with Biscuit |
| nf-core/cnvkit/coverage | cnvkit coverage BAM CRAM bedGraph read depth genomics | Calculate coverage in the given regions from BAM/CRAM or bedGraph files read depths. |
| nf-core/fastdup | duplicate BAM reads | FastDup is a tool designed to locate and tag duplicate reads in a coordinate-sorted SAM or BAM file, using the same core algorithm as Picard MarkDuplicates. |
| nf-core/smncopynumbercaller | copy number BAM CRAM SMN1 SMN2 | tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file. |