Nextflow Modules
Showing module(s) with keyword "quality control"
| Module | Keywords | Description |
|---|---|---|
| cellgeni/cellbender/qc | cellbender single-cell RNA-seq quality control ambient RNA | Collects summary statistics from CellBender outputs and produces a QC report directory with PDF plots and per-sample RDS summaries. |
| cellgeni/starsoloqc | STARsolo STAR QC quality control single-cell 10x RNA-seq | Collects QC statistics from STARsolo output directories, producing a merged TSV summary of alignment and cell-calling metrics across all samples in a dataset. |
| 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/busco/plot | genome fasta annotation busco transcriptome quality control | BUSCO summary plot generation using the built-in 'busco --plot' command |
| nf-core/chelae/trim | trimming quality control fastq adapter umi | Adapter and quality trimming of short-read FASTQ data using chelae. |
| nf-core/cnaqc | WGS copy number quality control | Quality control of copy number data from bulk WGS assays |
| nf-core/deepmased/features | metagenomics assembly quality control error detection deep learning features | DeepMAsED features subcommand: extracts alignment-based features from BAM and assembly FASTA for each contig, producing feature tables used as input for DeepMAsED predict. |
| nf-core/deepmased/predict | metagenomics assembly quality control error detection deep learning prediction | DeepMAsED predict subcommand: runs the pre-trained deep learning model on feature tables produced by DeepMAsED features to predict per-contig assembly error scores. |
| 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/eautils/fastqstats | fastq statistics quality control genomics | Calculate general and per-base statistics from FASTQ files |
| 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 |