Nextflow Modules
Showing module(s) with keyword "sam"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| 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_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_qc_picard | Workflow | statistics counts hs_metrics wgs_metrics bam sam cram | Produces comprehensive statistics from BAM file |
| nf-core/bam_sort_stats_samtools | Workflow | sort bam sam cram | Sort SAM/BAM/CRAM file |
| nf-core/bam_split_by_region | Workflow | split bam sam cram index | Split the reads in the input bam by specified genomic region. |
| nf-core/bam_stats_samtools | Workflow | statistics counts bam sam cram | Produces comprehensive statistics from SAM/BAM/CRAM file |
| nf-core/bam_subsampledepth_samtools | Workflow | subsample bam sam cram | Subsample a BAM/CRAM/SAM file using samtools to a given mean depth. "region", "subsample_fraction", "mean_depth" and "depth" keys will be added to the meta map to distinguish the different file generated and therefore shouldn't be used. The `depth` key will be added to the meta map of the output channel. |
| nf-core/bamtools/convert | Process | 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/bioawk | Process | bioawk fastq fasta sam file manipulation awk | Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats. |
| nf-core/bwafastalign/mem | Process | mem bwa bwafastalign alignment map fastq bam sam cram | Performs fastq alignment to a fasta reference using BWA-FastAlign. |
| nf-core/bwa/mem | Process | mem bwa alignment map fastq bam sam | Performs fastq alignment to a fasta reference using BWA |
| nf-core/bwamem2/mem | Process | mem bwa alignment map fastq bam sam | Performs fastq alignment to a fasta reference using BWA |
| nf-core/bwamem3/mem | Process | mem bwa alignment map fastq bam sam | Align fastq reads to a fasta reference using bwa-mem3 |
| nf-core/bwameme/mem | Process | mem |