Nextflow Modules
Showing module(s) with keyword "samtools"
| Module | Keywords | Description |
|---|---|---|
| nf-core/rustqc | rnaseq quality control qc bam dupradar featurecounts rseqc preseq qualimap samtools | All-in-one RNA-seq post-alignment QC replacing dupRadar, featureCounts biotype QC, RSeQC, Preseq, Qualimap, and SAMtools stats |
| nf-core/samtools/ampliconclip | amplicon clipping ampliconclip samtools | Clips read alignments where they match BED file defined regions |
| nf-core/samtools/bam2fq | bam2fq samtools fastq | The module uses bam2fq method from samtools to convert a SAM, BAM or CRAM file to FASTQ format |
| nf-core/samtools/bedcov | bedcov samtools coverage bed bam cram sam regions | reports coverage over regions in a supplied BED file |
| nf-core/samtools/collatefastq | bam2fq samtools fastq | The module uses collate and then fastq methods from samtools to convert a SAM, BAM or CRAM file to FASTQ format |
| nf-core/samtools/coverage | depth samtools bam | produces a histogram or table of coverage per chromosome |
| nf-core/samtools/depth | depth samtools statistics coverage | Computes the depth at each position or region. |
| nf-core/samtools/fixmate | fixmate samtools insert size repair bam paired read pairs | Samtools fixmate is a tool that can fill in information (insert size, cigar, mapq) about paired end reads onto the corresponding other read. Also has options to remove secondary/unmapped alignments and recalculate whether reads are proper pairs. |
| nf-core/samtools/markdup | bam duplicates markduplicates samtools | mark duplicate alignments in a coordinate sorted file |
| nf-core/telseq | bam cram genomics samtools telomere telseq | Telseq: a software for calculating telomere length |