Nextflow Modules
Showing module(s) with keyword "clipping"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bamclipper | Process | primer clipping genomics bam | This module is used to clip primer sequences from your alignments. |
| nf-core/bamutil/clipoverlap | Process | 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 | Process | 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/gatk4/cleansam | Process | clean bam gatk sam clipping | Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads |
| nf-core/leehom | Process | ancient DNA adapter removal clipping trimming merging collapsing preprocessing bayesian | Bayesian reconstruction of ancient DNA fragments |
| nf-core/picard/cleansam | Process | clean bam picard sam clipping | Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads |
| nf-core/samclip | Process | soft-clipped reads hard-clipped reads clipping genomics sam bam cram | Filters SAM/BAM/CRAM files for soft and hard clipped alignments |
| nf-core/samtools/ampliconclip | Process | amplicon clipping ampliconclip samtools | Clips read alignments where they match BED file defined regions |