Nextflow Modules
Showing module(s) with keyword "depth"
| Module | Keywords | Description |
|---|---|---|
| nf-core/blobtk/depth | bam gzipped blobtoolkit depth | Creates a bed file containing the depth of data at intervals of an aligned bam. |
| nf-core/deeptools/bamcoverage | coverage depth track | This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output. |
| nf-core/goleft/indexcov | coverage cnv genomics depth | Quickly estimate coverage from a whole-genome bam or cram index. A bam index has 16KB resolution so that's what this gives, but it provides what appears to be a high-quality coverage estimate in seconds per genome. |
| nf-core/jvarkit/wgscoverageplotter | bam cram depth coverage xml svg visualization | Plot whole genome coverage from BAM/CRAM file as SVG |
| nf-core/metabat2/jgisummarizebamcontigdepths | sort binning depth bam coverage de novo assembly | Depth computation per contig step of metabat2 |
| nf-core/metabat2/metabat2 | sort binning depth bam coverage de novo assembly | Metagenome binning of contigs |
| nf-core/paragraph/idxdepth | bam cram depth paragraph | Determines the depth in a BAM/CRAM file |
| nf-core/perbase | bam cram depth | Per-base metrics on BAM/CRAM files. |
| nf-core/rasusa | coverage depth subsampling | Randomly subsample sequencing reads to a specified coverage |
| nf-core/sambamba/depth | depth coverage sambamba | Outputs a coverage file from bam files |
| nf-core/samtools/coverage | depth samtools bam | produces a histogram or table of coverage per chromosome |
| nf-core/samtools/depth | depth samtools statistics coverage | Computes the depth at each position or region. |