Nextflow Modules
Showing module(s) with keyword "sam"
| Module | Keywords | Description |
|---|---|---|
| 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/bioawk | 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/bwa/mem | mem bwa alignment map fastq bam sam | Performs fastq alignment to a fasta reference using BWA |
| nf-core/bwamem2/mem | mem bwa alignment map fastq bam sam | Performs fastq alignment to a fasta reference using BWA |
| 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/bwa/sampe | bwa aln short-read align reference fasta map sam bam | Convert paired-end bwa SA coordinate files to SAM format |
| nf-core/bwa/samse | bwa aln short-read align reference fasta map sam bam | Convert bwa SA coordinate file to SAM format |
| nf-core/chromap/chromap | chromap alignment map fastq bam sam hi-c atac-seq chip-seq trimming duplicate removal | Performs preprocessing and alignment of chromatin fastq files to fasta reference files using chromap. |
| nf-core/crumble | compress bam sam cram | Controllable lossy compression of BAM/CRAM files |
| nf-core/dragmap/align | alignment map fastq bam sam | Performs fastq alignment to a reference using DRAGMAP |
| nf-core/elprep/filter | sort bam sam filter variant calling | Filter, sort and markdup sam/bam files, with optional BQSR and variant calling. |
| nf-core/elprep/merge | bam sam merge | Merge split bam/sam chunks in one file |
| nf-core/fgbio/sortbam | sort bam sam | Sorts a SAM or BAM file. Several sort orders are available, including coordinate, queryname, random, and randomquery. |
| nf-core/gatk4/calibratedragstrmodel | gatk4 bam cram sam calibratedragstrmodel | estimates the parameters for the DRAGstr model |
| nf-core/gatk4/printreads | bam cram gatk4 printreads sam | Print reads in the SAM/BAM/CRAM file |
| nf-core/gatk4/revertsam | gatk4 revert sam | Reverts SAM or BAM files to a previous state. |
| nf-core/homer/maketagdirectory |