Nextflow Modules
Showing module(s) with keyword "alignment"
| Module | Keywords | Description |
|---|---|---|
| nf-core/abra2 | alignment realignment indels bam dna rna splice-junctions assembly | Assembly Based ReAligner for next-generation sequencing data |
| nf-core/alignoth | genomics alignment visualization pileup plotting | Creating alignment plots from bam files |
| nf-core/amps | malt MaltExtract HOPS amps alignment metagenomics ancient DNA aDNA palaeogenomics archaeogenomics microbiome authentication damage edit distance post Post-processing visualisation | Post-processing script of the MaltExtract component of the HOPS package |
| nf-core/ashlar | image_processing alignment registration | Alignment by Simultaneous Harmonization of Layer/Adjacency Registration |
| nf-core/busco/phylogenomics | phylogenies orthologs alignment | Construct species phylogenies using BUSCO proteins |
| nf-core/bwafastalign/mem | mem bwa bwafastalign alignment map fastq bam sam cram | Performs fastq alignment to a fasta reference using BWA-FastAlign. |
| nf-core/bwa/mem | mem bwa alignment map fastq bam sam | Performs fastq alignment to a fasta reference using BWA |
| nf-core/bwamem2/mem | mem bwa alignment map fastq bam sam | Performs fastq alignment to a fasta reference using BWA |
| nf-core/bwameme/mem | mem bwa bwamem2 bwameme alignment map fastq bam sam cram | Performs fastq alignment to a fasta reference using BWA-MEME |
| nf-core/bwameth/align | bwameth alignment 3-letter genome map methylation 5mC methylseq bisulphite bisulfite fastq bam | Performs alignment of BS-Seq reads using bwameth |
| nf-core/cdhit/cdhit | cluster protein alignment fasta | Cluster protein sequences using sequence similarity |
| nf-core/cdhit/cdhitest | cluster nucleotide alignment fasta | Cluster nucleotide sequences using sequence similarity |
| nf-core/chromap/chromap | chromap alignment map fastq bam sam hi-c atac-seq chip-seq trimming duplicate removal | Performs preprocessing and alignment of chromatin fastq files to fasta reference files using chromap. |
| nf-core/clipkit | alignment trimming phylogeny | A multiple sequence alignment-trimming algorithm for accurate phylogenomic inference. |
| nf-core/clustalo/align | alignment MSA genomics | Align sequences using Clustal Omega |
| nf-core/clusty | cluster network contig scaffold alignment protein | Clusty is a tool for large-scale clustering using sparse distance matrices, suitable for datasets with millions of objects. |
| nf-core/cmaple | phylogeny phylogenetic tree maximum likelihood dna amino acid alignment tree reconstruction cmaple iqtree | Efficient phylogenetic tree reconstruction for sequences using the CMAPLE algorithm |
| nf-core/diamond/cluster | clustering alignment genomics proteomics | calculate clusters of highly similar sequences |
| nf-core/disambiguate | disambiguation xenograft explant rna-seq alignment bam | Disambiguates reads aligned to two different organisms (e.g. human and mouse) from the same source of FASTQ files. Useful in explant RNA/DNA-Seq workflows where reads from two species are present. For reads aligned to both organisms, the algorithm compares alignment quality scores to determine the most likely species of origin. Produces four BAM files (uniquely assigned to species A or B, ambiguous for species A or B) and a summary file. |
| nf-core/dragmap/align | alignment map fastq bam sam | Performs fastq alignment to a reference using DRAGMAP |