Nextflow Modules
Showing module(s) with keyword "bam"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/abra2 | Process | alignment realignment indels bam dna rna splice-junctions assembly | Assembly Based ReAligner for next-generation sequencing data |
| nf-core/ascat | Process | bam copy number cram | copy number profiles of tumour cells. |
| nf-core/atlas/pmd | Process | ancient DNA post mortem damage bam | Estimate the post-mortem damage patterns of DNA |
| nf-core/atlas/splitmerge | Process | split merge bam read group | split single end read groups by length and merge paired end reads |
| nf-core/bamaligncleaner | Process | bam clean align | removes unused references from header of sorted BAM/CRAM files. |
| nf-core/bam_applybqsr | Workflow | bam cram bqsr recalibration gatk4 | Apply Base Quality Score Recalibration (BQSR) to a BAM or CRAM file using GATK4 ApplyBQSR. Supports scatter-gather across genomic intervals: when more than one interval file is supplied per sample, the interval-level outputs are merged back together with samtools merge. When no intervals are supplied (num_intervals: 0), ApplyBQSR is run once on the whole input and no merge step is performed. |
| nf-core/bamclipper | Process | primer clipping genomics bam | This module is used to clip primer sequences from your alignments. |
| nf-core/bam_cnv_wisecondorx | Workflow | cnv bam bed cram plots genomics | A subworkflow for calling CNVs using WisecondorX |
| nf-core/bam_dedup_stats_samtools_umicollapse | Workflow | umi dedup index bam sam cram | umicollapse, index BAM file and run samtools stats, flagstat and idxstats |
| nf-core/bam_dedup_stats_samtools_umitools | Workflow | umi dedup index bam sam cram | UMI-tools dedup, index BAM file and run samtools stats, flagstat and idxstats |
| nf-core/bam_docounts_contamination_angsd | Workflow | angsd bam contamination docounts | Calculate contamination of the X-chromosome with ANGSD |
| nf-core/bam_impute_quilt2 | Workflow | bam cram imputation quilt quilt2 vcf | Impute low-coverage BAM or CRAM inputs with QUILT2 and ligate chunked outputs per chromosome. "regionout", "regionoutPadded", "regionSize" keys will be added to the meta map to distinguish the different files before ligation and therefore should not be used. |
| nf-core/bam_markduplicates_picard | Workflow | markduplicates bam sam cram | Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats |
| nf-core/bam_markduplicates_samtools | Workflow | markdup bam sam cram | Samtools markduplicate SAM/BAM/CRAM file |
| nf-core/bam_methyldackel | Workflow | 3-letter genome methylation 5mC methylseq bisulphite bisulfite bam | Performs methylation quantification based on negative readout of C to T conversion of 3-letter genome alignments using Methyldackel. |
| nf-core/bam_ngscheckmate | Workflow | ngscheckmate qc bam snp | Take a set of bam files and run NGSCheckMate to determine whether samples match with each other, using a set of SNPs. |
| nf-core/bam_qc_picard | Workflow | statistics counts hs_metrics wgs_metrics bam sam cram | Produces comprehensive statistics from BAM file |
| nf-core/bam_qc_rnaseq | Workflow </ |