Nextflow Modules
Showing module(s) with keyword "bam"
| Module | Keywords | Description |
|---|---|---|
| nf-core/abra2 | alignment realignment indels bam dna rna splice-junctions assembly | Assembly Based ReAligner for next-generation sequencing data |
| nf-core/ascat | bam copy number cram | copy number profiles of tumour cells. |
| nf-core/atlas/pmd | ancient DNA post mortem damage bam | Estimate the post-mortem damage patterns of DNA |
| nf-core/atlas/splitmerge | split merge bam read group | split single end read groups by length and merge paired end reads |
| nf-core/bamaligncleaner | bam clean align | removes unused references from header of sorted BAM/CRAM files. |
| nf-core/bamclipper | primer clipping genomics bam | This module is used to clip primer sequences from your alignments. |
| nf-core/bamstats/generalstats | bam statistics genomics | write your description here |
| nf-core/bamtofastq10x | bam convert fastq 10x | Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis |
| nf-core/bamtools/convert | bamtools bamtools/convert bam convert bed fasta fastq json pileup sam yaml | BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. |
| nf-core/bamtools/split | bamtools bamtools/split bam split chunk | BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. |
| nf-core/bamtools/stats | bamtools stats bam | BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. |
| nf-core/bamutil/clipoverlap | bam clipping clipOverlap bamUtil | clips overlapping read pairs. When two mates overlap, this tool will clip the record's whose clipped region would have the lowest average quality. |
| nf-core/bamutil/trimbam | bam trim clipping bamUtil trimBam | trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping |
| nf-core/bedtools/bamtobed | bam bed bedtools bamtobed converter | Converts a bam file to a bed12 file. |
| nf-core/bedtools/coverage | bedtools coverage bam bed gff vcf histogram | computes both the depth and breadth of coverage of features in file B on the features in file A |
| nf-core/bedtools/genomecov | bed bam genomecov bedtools histogram | Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome. |
| nf-core/biobambam/bammarkduplicates2 | markduplicates bam cram | Locate and tag duplicate reads in a BAM file |
| nf-core/biobambam/bammerge | merge bam sorted | Merge a list of sorted bam files |
| nf-core/biobambam/bamsormadup | markduplicates sort bam cram | Parallel sorting and duplicate marking |
| nf-core/biscuit/align | biscuit DNA methylation WGBS scWGBS |