Nextflow Modules
Showing module(s) with keyword "reference"
| Module | Keywords | Description |
|---|---|---|
| nf-core/arriba/download | fusion arriba reference | Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. |
| nf-core/bbmap/align | align map fasta fastq genome reference | Align short or PacBio reads to a reference genome using BBMap |
| nf-core/bbmap/bbsplit | align map fastq genome reference | Split sequencing reads by mapping them to multiple references simultaneously |
| nf-core/biscuit/index | biscuit DNA methylation WGBS scWGBS bisulfite sequencing index reference fasta | Indexes a reference genome for use with Biscuit |
| nf-core/bowtie2/align | align map fasta fastq genome reference | Align reads to a reference genome using bowtie2 |
| nf-core/bowtie2/build | build index fasta genome reference | Builds bowtie index for reference genome |
| nf-core/bowtie/align | align map fastq fasta genome reference | Align reads to a reference genome using bowtie |
| nf-core/bowtie/build | index fasta genome reference | Create bowtie index for reference genome |
| nf-core/bwa/aln | bwa aln short-read align reference fasta map fastq | Find SA coordinates of the input reads for bwa short-read mapping |
| nf-core/bwa/index | index fasta genome reference | Create BWA index for reference genome |
| nf-core/bwamem2/index | index fasta genome reference | Create BWA-mem2 index for reference genome |
| nf-core/bwameme/index | index fasta genome reference | Create BWA-MEME index for reference genome |
| nf-core/bwa/sampe | bwa aln short-read align reference fasta map sam bam | Convert paired-end bwa SA coordinate files to SAM format |
| nf-core/bwa/samse | bwa aln short-read align reference fasta map sam bam | Convert bwa SA coordinate file to SAM format |
| nf-core/cellrangerarc/count | align count reference | Module to use Cell Ranger's ARC pipelines analyze sequencing data produced from Chromium Single Cell ARC. Uses the cellranger-arc count command. |
| 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/cellrangerarc/mkgtf | reference mkref index | Module to build a filtered gtf needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkgtf command. |
| nf-core/cellrangerarc/mkref | reference mkref index | Module to build the reference needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkref command. |
| nf-core/cellrangeratac/count | align |