Nextflow Modules
Showing module(s) with keyword "quality control"
| Module | Keywords | Description |
|---|---|---|
| nf-core/biscuit/qc | biscuit DNA methylation WGBS scWGBS bisulfite sequencing index BAM quality control | Perform basic quality control on a BAM file generated with Biscuit |
| nf-core/busco/busco | quality control genome transcriptome proteome | Benchmarking Universal Single Copy Orthologs |
| nf-core/busco/download | quality control genome transcriptome proteome | Download database for BUSCO |
| nf-core/busco/generateplot | genome fasta annotation busco transcriptome quality control | BUSCO plot generation tool |
| nf-core/cnaqc | WGS copy number quality control | Quality control of copy number data from bulk WGS assays |
| nf-core/dragen/germline | check fingerprint copy number variation fastqc genomics germline quality control repeat expansion detection structural variation trimming variable number tandem repeat detection variant annotation variant calling variant deduplication | The DRAGEN DNA Germline Pipeline accelerates the secondary analysis of NGS data by harnessing the tremendous power available on the DRAGEN Platform. The pipeline includes highly optimized algorithms for mapping, aligning, sorting, duplicate marking, and haplotype variant calling. In addition to haplotype variant calling, the pipeline supports calling of copy number and structural variants as well as detection of repeat expansions and targeted calls. |
| nf-core/falco | quality control qc adapters fastq | Run falco on sequenced reads |
| nf-core/faqcs | trimming quality control fastq faqcs | Perform adapter and quality trimming on sequencing reads with reporting |
| nf-core/fastp | trimming quality control fastq | Perform adapter/quality trimming on sequencing reads |
| nf-core/fastplong | trimming quality control fastq long reads | Perform adapter/quality trimming and QC on long sequencing reads (ONT, PacBio, etc.) |
| nf-core/fastqc | quality control qc adapters fastq | Run FastQC on sequenced reads |
| nf-core/fastqe | quality control fastq emoji visualization | fastqe is a bioinformatics command line tool that uses emojis to represent and analyze genomic data. |
| nf-core/fcs/fcsadaptor | assembly genomics quality control contamination NCBI | Run NCBI's FCS adaptor on assembled genomes |
| nf-core/fcs/fcsgx | assembly genomics quality control contamination NCBI | Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid. |
| nf-core/filtlong | nanopore quality control QC filtering long reads short reads | Filtlong filters long reads based on quality measures or short read data. |
| nf-core/gunc/downloaddb | download prokaryote assembly genome quality control chimeras | Download database for GUNC detection of Chimerism and Contamination in Prokaryotic Genomes |
| nf-core/gunc/mergecheckm | gunc checkm summary prokaryote assembly genome quality control chimeras | Merging of CheckM and GUNC results in one summary table |