Nextflow Modules
Showing module(s) with keyword "cram"
| Module | Keywords | Description |
|---|---|---|
| nf-core/ascat | bam copy number cram | copy number profiles of tumour cells. |
| nf-core/biobambam/bammarkduplicates2 | markduplicates bam cram | Locate and tag duplicate reads in a BAM file |
| nf-core/biobambam/bamsormadup | markduplicates sort bam cram | Parallel sorting and duplicate marking |
| nf-core/bwameme/mem | mem bwa bwamem2 bwameme alignment map fastq bam sam cram | Performs fastq alignment to a fasta reference using BWA-MEME |
| nf-core/crumble | compress bam sam cram | Controllable lossy compression of BAM/CRAM files |
| nf-core/expansionhunter | STR repeat_expansions bam cram vcf json | Estimate repeat sizes using NGS data |
| nf-core/expansionhunterdenovo/profile | expansionhunterdenovo profile STR genome bam cram | Compute genome-wide STR profile |
| nf-core/fgbio/fastqtobam | unaligned bam cram | Using the fgbio tools, converts FASTQ files sequenced into unaligned BAM or CRAM files possibly moving the UMI barcode into the RX field of the reads |
| nf-core/gangstr | gangstr STR bam cram vcf | GangSTR is a tool for genome-wide profiling tandem repeats from short reads. |
| nf-core/gatk4/applybqsr | bam base quality score recalibration bqsr cram gatk4 | Apply base quality score recalibration (BQSR) to a bam file |
| nf-core/gatk4/calibratedragstrmodel | gatk4 bam cram sam calibratedragstrmodel | estimates the parameters for the DRAGstr model |
| nf-core/gatk4/collectreadcounts | collectreadcounts bam cram gatk4 | Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval. |
| nf-core/gatk4/printreads | bam cram gatk4 printreads sam | Print reads in the SAM/BAM/CRAM file |
| nf-core/gatk4spark/applybqsr | bam base quality score recalibration bqsr cram gatk4spark | Apply base quality score recalibration (BQSR) to a bam file |
| nf-core/gatk4/splitcram | cram gatk4 split splitcram | Splits CRAM files efficiently by taking advantage of their container based structure |
| nf-core/goleft/indexsplit | bam bed cram index split | Quickly generate evenly sized (by amount of data) regions across a number of bam/cram files |
| nf-core/graphtyper/genotype | variant vcf bam cram pangenome | Tools for population-scale genotyping using pangenome graphs. |
| nf-core/gridss/gridss | gridss structural variants bam cram vcf | GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. |
| nf-core/jvarkit/wgscoverageplotter | bam cram depth coverage xml svg visualization | Plot whole genome coverage from BAM/CRAM file as SVG |