Nextflow Modules
Showing module(s) with keyword "reads"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/fastdup | Process | duplicate BAM reads | FastDup is a tool designed to locate and tag duplicate reads in a coordinate-sorted SAM or BAM file, using the same core algorithm as Picard MarkDuplicates. |
| nf-core/fastq_shortreads_preprocess_qc | Workflow | fastq illumina short reads qc stats preprocessing barcoding adapters merge complexity deduplication host decontamination | Quality check and preprocessing subworkflow of Illumina short reads that can do: quality check of input reads and generate statistics, preprocess and validate reads, barcode removal, remove adapters and merge reads, filter by sequence complexity, deduplicate reads, remove host contamination, concatenate reads and generate statistics for post-processing reads. WARNING: requires at least the process configurations from the nextflow.config to be added to the modules.config in the pipeline in order to work as intended. |
| nf-core/holodeck/simulate | Process | simulation fastq reads sequencing benchmarking | Simulate sequencing reads from a reference genome with holodeck |
| nf-core/khmer/trimlowabund | Process | quality control genomics filtering reads khmer k-mer | Removes low abundance k-mers from FASTA/FASTQ files |
| nf-core/kma/index | Process | alignment kma index database reads | This module wraps the index module of the KMA alignment tool. |
| nf-core/kma/kma | Process | fastq reads alignment kma | Mapping raw reads directly against redundant databases via KMA alignment |
| nf-core/mtnucratio | Process | mtnucratio ratio reads bam mitochondrial to nuclear ratio mitochondria statistics | A small Java tool to calculate ratios between MT and nuclear sequencing reads in a given BAM file. |
| nf-core/seqkit/head | Process | filter subset reads fasta fastq seqkit | Subset FASTA/FASTQ files to some number of sequences |
| nf-core/seqtk/sample | Process | sample fastx reads | Subsample reads from FASTQ files |
| nf-core/wgsim | Process | simulate fasta reads | simulating sequence reads from a reference genome |