Nextflow Modules
Showing module(s) with keyword "samtools"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/fastq_create_umi_consensus_fgbio | Workflow | fgbio umi samblaster samtools bwa | This workflow uses the suite FGBIO to identify and remove UMI tags from FASTQ reads convert them to unmapped BAM file, map them to the reference genome, and finally use the mapped information to group UMIs and generate consensus reads in each group |
| nf-core/rustqc | Process | 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 | Process | amplicon clipping ampliconclip samtools | Clips read alignments where they match BED file defined regions |
| nf-core/samtools/bam2fq | Process | 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 | Process | bedcov samtools coverage bed bam cram sam regions | reports coverage over regions in a supplied BED file |
| nf-core/samtools/collatefastq | Process | 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 | Process | depth samtools bam | produces a histogram or table of coverage per chromosome |
| nf-core/samtools/depth | Process | depth samtools statistics coverage | Computes the depth at each position or region. |
| nf-core/samtools/fixmate | Process | 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 | Process | bam duplicates markduplicates samtools | mark duplicate alignments in a coordinate sorted file |
| nf-core/samtools/trimheader | Process | bam header reference samtools | Remove @SQ header lines for references without any reads, keeping every read. Some tools, such as featureCounts, cannot read a BAM header over 2 GiB, which a very fragmented assembly produces. |
| nf-core/telseq | Process | bam cram genomics samtools telomere telseq | Telseq: a software for calculating telomere length |