Nextflow Modules
Showing module(s) with keyword "duplicates"
| Module | Keywords | Description |
|---|---|---|
| nf-core/dupblaster | 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/fgumi/dedup | UMIs deduplication duplicates bam | Mark or remove PCR duplicates using UMI information with fgumi |
| nf-core/parabricks/fq2bam | align sort bqsr duplicates | NVIDIA Clara Parabricks GPU-accelerated alignment, sorting, BQSR calculation, and duplicate marking. Note this nf-core module requires files to be copied into the working directory and not symlinked. |
| nf-core/parabricks/fq2bammeth | align sort bqsr duplicates bwameth | NVIDIA Clara Parabricks GPU-accelerated fast, accurate algorithm for mapping methylated DNA sequence reads to a reference genome, performing local alignment, and producing alignment for different parts of the query sequence |
| nf-core/parabricks/minimap2 | align sort bqsr duplicates long read | NVIDIA Clara Parabricks GPU-accelerated minimap2 for aligning long read sequences against a large reference database using an accelerated KSW2 to convert FASTQ to BAM/CRAM. |
| nf-core/picard/markduplicates | markduplicates pcr duplicates bam sam cram | Locate and tag duplicate reads in a BAM file |
| nf-core/sambamba/markdup | markduplicates duplicates bam | find and mark duplicate reads in BAM file |
| nf-core/samtools/markdup | bam duplicates markduplicates samtools | mark duplicate alignments in a coordinate sorted file |
| nf-core/seqkit/rmdup | genomics fasta fastq remove duplicates | Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...) |