Nextflow Modules
Showing module(s) with keyword "markduplicates"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_markduplicates_picard | Workflow | markduplicates bam sam cram | Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats |
| nf-core/biobambam/bammarkduplicates2 | Process | markduplicates bam cram | Locate and tag duplicate reads in a BAM file |
| nf-core/biobambam/bamsormadup | Process | markduplicates sort bam cram | Parallel sorting and duplicate marking |
| nf-core/dupblaster | Process | duplicates markduplicates bam alignment | Streaming duplicate marking for NGS alignments with dupblaster; for maximum throughput it can also run inline in the alignment pipe (aligner | dupblaster | sort) rather than as a standalone step |
| nf-core/gatk4/markduplicates | Process | bam gatk4 markduplicates sort | This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. |
| nf-core/gatk4spark/markduplicates | Process | bam gatk4spark markduplicates sort | This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. |
| nf-core/picard/markduplicates | Process | markduplicates pcr duplicates bam sam cram | Locate and tag duplicate reads in a BAM file |
| nf-core/sambamba/markdup | Process | markduplicates duplicates bam | find and mark duplicate reads in BAM file |
| nf-core/samtools/markdup | Process | bam duplicates markduplicates samtools | mark duplicate alignments in a coordinate sorted file |
| nf-core/samtools/sormadup | Process | cat collate fixmate sort markduplicates bam sam cram multi-tool | Collate/Fixmate/Sort/Markdup SAM/BAM/CRAM file |