Nextflow Modules
Showing module(s) with keyword "coverage"
| Module | Keywords | Description |
|---|---|---|
| nf-core/allelecounter | allele count coverage | Generates a count of coverage of alleles |
| nf-core/bbmap/bbnorm | normalization assembly coverage | BBNorm is designed to normalize coverage by down-sampling reads over high-depth areas of a genome, to result in a flat coverage distribution. |
| nf-core/bbmap/pileup | fasta genome coverage | Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file. |
| nf-core/bedtools/coverage | bedtools coverage bam bed gff vcf histogram | computes both the depth and breadth of coverage of features in file B on the features in file A |
| nf-core/cmseq/polymut | polymut polymorphic mags assembly polymorphic sites estimation protein coding genes cmseq bam coverage | Calculates polymorphic site rates over protein coding genes |
| nf-core/concoct/concoctcoveragetable | contigs fragment mags binning bed bam subcontigs coverage | Generate the input coverage table for CONCOCT using a BEDFile |
| nf-core/coverm/contig | mapping genomics metagenomics coverage | Map reads to contigs and estimate coverage |
| nf-core/coverm/genome | mapping genomics metagenomics coverage | Calculate read coverage per-genome |
| 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/deeptools/bigwigcompare | bigwig compare genomics deeptools coverage | Compare two bigWig files based on the number of mapped reads |
| nf-core/deeptools/multibamsummary | bam coverage genome bin | Computes read coverage for genomic regions (bins) across the entire genome. |
| nf-core/eigenstratdatabasetools/eigenstratsnpcoverage | coverage eigenstrat eigenstratdatabasetools snp snps | Provide the SNP coverage of each individual in an eigenstrat formatted dataset. |
| nf-core/fairy/coverage | metagenomics coverage binning alignment-free contig | Computes coverage depth statistics for assembled contigs from one or more fairy sketch files, producing a MetaBAT2-compatible TSV with per-contig mean depth and variance columns. |
| nf-core/fairy/sketch | sketch coverage fastq alignment-free metagenomics | Sketches FASTQ reads into binary sketch (.bcsp) files for alignment-free coverage estimation. |
| nf-core/fastcov | coverage bam map | Generate a coverage plot from one or more bam files |
| 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/instrain/compare | instrain compare align diversity coverage | Strain-level comparisons across multiple inStrain profiles |
| 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 |