Nextflow Modules
Showing module(s) with keyword "sort"
| Module | Keywords | Description |
|---|---|---|
| nf-core/bedtools/sort | bed sort bedtools chromosome | Sorts a feature file by chromosome and other criteria. |
| nf-core/biobambam/bamsormadup | markduplicates sort bam cram | Parallel sorting and duplicate marking |
| nf-core/clame | sort genomics binning metagenomics | binning of metagenomic sequences |
| nf-core/crisprcleanr/normalize | sort CNV correction CRISPR | remove false positives of functional crispr genomics due to CNVs |
| nf-core/csvtk/sort | sort tsv csv | Sort CSV (or TSV) tables |
| nf-core/duphold | sort duphold structural variation depth information | SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. This can be used as additional information for filtering variants; for example we will be skeptical of deletion calls that do not have lower than average coverage compared to regions with similar gc-content. |
| nf-core/elprep/filter | sort bam sam filter variant calling | Filter, sort and markdup sam/bam files, with optional BQSR and variant calling. |
| nf-core/fgbio/sortbam | sort bam sam | Sorts a SAM or BAM file. Several sort orders are available, including coordinate, queryname, random, and randomquery. |
| nf-core/flash | sort reads merging merge mate pairs | Perform merging of mate paired-end sequencing reads |
| nf-core/fusionreport/detect | sort RNA-seq fusion report detect | fusionreport_detect |
| nf-core/fusionreport/download | sort RNA-seq fusion_report download | Build DB for fusionreport |
| nf-core/gappa/examinegraft | sort graft phylogeny | Grafts query sequences from phylogenetic placement on the reference tree |
| nf-core/gatk4/baserecalibrator | base quality score recalibration table bqsr gatk4 sort | Generate recalibration table for Base Quality Score Recalibration (BQSR) |
| nf-core/gatk4/gatherpileupsummaries | gatk4 mpileup sort | write your description here |
| nf-core/gatk4/intervallisttools | bed gatk4 interval_list sort | Splits the interval list file into unique, equally-sized interval files and place it under a directory |
| nf-core/gatk4/markduplicates | 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/baserecalibrator | base quality score recalibration table bqsr gatk4spark sort | Generate recalibration table for Base Quality Score Recalibration (BQSR) |
| nf-core/gatk4spark/markduplicates | 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/gnu/sort | GNU coreutils sort merge compare | Writes a sorted concatenation of file/s |
| nf-core/gtfsort | sort genomics gtf | Sort GTF files in chr/pos/feature order |