Nextflow Modules
Showing module(s) with keyword "illumina"
| Module | Keywords | Description |
|---|---|---|
| nf-core/artic/aligntrim | artic primer trimming amplicon genomics sequencing nanopore illumina | Standalone version of fieldbioinformatics aligntrim. Soft clips amplicon scheme primer sites in BAM/SAM files. |
| nf-core/art/illumina | fastq fasta illumina simulate | Simulation tool to generate synthetic Illumina next-generation sequencing reads |
| nf-core/bcl2fastq | demultiplex illumina fastq | Demultiplex Illumina BCL files |
| nf-core/bclconvert | demultiplex illumina fastq | Demultiplex Illumina BCL files |
| nf-core/cellrangerarc/mkfastq | reference mkfastq fastq illumina bcl2fastq | Module to create fastqs needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkfastq command. |
| nf-core/cellrangeratac/mkfastq | reference mkfastq fastq illumina bcl2fastq | Module to create fastqs needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkfastq command. |
| nf-core/cellranger/mkfastq | reference mkfastq fastq illumina bcl2fastq | Module to create FASTQs needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkfastq command. |
| nf-core/getorganelle/fromreads | assembly organelle mitochondria illumina | Assembles organelle genomes from genomic data |
| nf-core/hypo | assembly polishing nanopore illumina | Assembly polisher using short (and long) reads |
| nf-core/samshee | samplesheet illumina bclconvert bcl2fastq | Module to validate illumina® Sample Sheet v2 files. |
| nf-core/shovill | bacterial assembly illumina | Assemble bacterial isolate genomes from Illumina paired-end reads |
| nf-core/srst2/srst2 | mlst typing illumina | Short Read Sequence Typing for Bacterial Pathogens is a program designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes. |