Nextflow Modules
Showing module(s) with keyword "align"
| Module | Keywords | Description |
|---|---|---|
| nf-core/ampcombi | antimicrobial peptides amps parsing reporting align macrel amplify hmmsearch neubi ampir DRAMP | A tool to parse and summarise results from antimicrobial peptides tools and present functional classification. |
| nf-core/ampcombi2/cluster | antimicrobial peptides amps parsing reporting align clustering mmseqs2 | A submodule that clusters the merged AMP hits generated from ampcombi2/parsetables and ampcombi2/complete using MMseqs2 cluster. |
| nf-core/ampcombi2/complete | antimicrobial peptides amps parsing reporting align macrel amplify hmmsearch neubi ampir ampgram amptransformer DRAMP | A submodule that merges all output summary tables from ampcombi/parsetables in one summary file. |
| nf-core/ampcombi2/parsetables | antimicrobial peptides amps parsing reporting align macrel amplify hmmsearch neubi ampir ampgram amptransformer DRAMP MMseqs2 InterProScan | A submodule that parses and standardizes the results from various antimicrobial peptide identification tools. |
| nf-core/bamaligncleaner | bam clean align | removes unused references from header of sorted BAM/CRAM files. |
| 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/bowtie2/align | align map fasta fastq genome reference | Align reads to a reference genome using bowtie2 |
| nf-core/bowtie/align | align map fastq fasta genome reference | Align reads to a reference genome using bowtie |
| 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/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/cellrangeratac/count | align count reference | Module to use Cell Ranger's ATAC pipelines analyze sequencing data produced from Chromium Single Cell ATAC. |
| nf-core/cellranger/count | align count reference | Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression. |
| nf-core/cellranger/multi | align reference cellranger multiomics gene expression vdj antigen capture antibody capture crispr | Module to use Cell Ranger's pipelines to analyze sequencing data produced from various Chromium technologies, including Single Cell Gene Expression, Single Cell Immune Profiling, Feature Barcoding, and Cell Multiplexing. |
| nf-core/cellranger/vdj | align vdj reference immunoprofiling single-cell cellranger | Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Immune Profiling. |
| nf-core/fastqscreen/fastqscreen | align map fasta fastq genome reference | Align reads to multiple reference genomes using fastq-screen |
| nf-core/graphmap2/align | align fasta fastq genome reference | A versatile pairwise aligner for genomic and spliced nucleotide sequences |
| nf-core/hisat2/align | align fasta genome reference | Align RNA-Seq reads to a reference with HISAT2 |