Nextflow Modules
Showing module(s) with keyword "qc"
| Module | Keywords | Description |
|---|---|---|
| nf-core/ataqv/ataqv | ATAC-seq qc ataqv | ataqv function of a corresponding ataqv tool |
| nf-core/ataqv/mkarv | ataqv ATAC-seq qc mkarv | mkarv function of a corresponding ataqv tool |
| nf-core/bismark/report | bismark qc methylation 5mC methylseq bisulphite bisulfite report | Collects bismark alignment reports |
| nf-core/bismark/summary | bismark qc methylation 5mC methylseq bisulphite bisulfite report summary | Uses Bismark report files of several samples in a run folder to generate a graphical summary HTML report. |
| nf-core/chopper | filter trimming fastq nanopore qc | Filter and trim long read data. |
| nf-core/custom/collectstats | stats collect summary qc | Collects per-sample read-processing statistics (trimming, decontamination, alignment, feature counting, and optionally taxonomy/function summaries) from a set of heterogeneous log/table files into a single overall-stats table per run. |
| nf-core/custom/multiqccustombiotype | biotype featurecounts multiqc rnaseq qc | Generate MultiQC-compatible biotype count summaries from featureCounts output |
| nf-core/falco | quality control qc adapters fastq | Run falco on sequenced reads |
| nf-core/fastaguard | fasta assembly qc | FASTA preflight QC for assembly pipelines |
| nf-core/fastqc | quality control qc adapters fastq | Run FastQC on sequenced reads |
| nf-core/ltrretriever/lai | genomics annotation repeat long terminal retrotransposon retrotransposon stats qc | Estimates the mean LTR sequence identity in the genome. The input genome fasta should have short alphanumeric IDs without comments |
| nf-core/merqury/hapmers | genomics quality check qc kmer | A script to generate hap-mer dbs for trios |
| nf-core/methyldackel/mbias | methylation 5mC methylseq bisulphite bisulfite methylation bias mbias qc bam cram | Generates methylation bias plots from alignments |
| nf-core/methylsieve | methylation bisulfite em-seq unconverted bam qc | Filter/tag unconverted reads in methylation sequencing with methylsieve; for maximum throughput it can also run inline in the alignment pipe (aligner | methylsieve | sort) rather than as a standalone step |
| nf-core/nacho/normalize | nacho nanostring mRNA miRNA qc | NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data. NanoString nCounter data is a messenger-RNA/micro-RNA (mRNA/miRNA) expression assay and works with fluorescent barcodes. Each barcode is assigned a mRNA/miRNA, which can be counted after bonding with its target. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA. |
| nf-core/nacho/qc | nacho nanostring mRNA miRNA qc | NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data. NanoString nCounter data is a messenger-RNA/micro-RNA (mRNA/miRNA) expression assay and works with fluorescent barcodes. Each barcode is assigned a mRNA/miRNA, which can be counted after bonding with its target. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA. |
| nf-core/nanocomp | bam fasta fastq qc nanopore | Compare multiple runs of long read sequencing data and alignments |
| nf-core/nanoplot |