Nextflow Modules
Showing module(s) with keyword "kmer"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/arcane/index | Process | single-cell rnaseq index kmer hash transcriptomics | Build a k-mer hash index from a filtered reference for alignment-free single-cell RNA-seq quantification with Arcane |
| nf-core/cobiontid/kmercounter | Process | cobiontid kmer counts npy fasta | A rust based tool based on Needletail's FASTA parser tallies k-mer counts for large sequencing rounds. Written with downstream processing with Tensorflow or numpy in mind. |
| nf-core/concoct/concoct | Process | contigs fragment mags binning concoct kmer nucleotide composition metagenomics bins | Unsupervised binning of metagenomic contigs by using nucleotide composition - kmer frequencies - and coverage data for multiple samples |
| nf-core/genometester4/glistmaker | Process | kmer sort alignment-free | Create and count k-mer lists from nucelotide sequences. |
| nf-core/mashmap | Process | mapper aligner minhash kmer | Mashmap is an approximate long read or contig mapper based on Jaccard similarity |
| nf-core/merquryfk/ploidyplot | Process | kmer smudgeplot ploidy | An improved version of Smudgeplot using FastK |
| nf-core/merqury/hapmers | Process | genomics quality check qc kmer | A script to generate hap-mer dbs for trios |
| nf-core/metacache/build | Process | genomics metagenomics taxonomy short reads long reads kmer k-mer metacache build reference | Taxonomic profiling database building with MetaCache |
| nf-core/ska/distance | Process | genomics metagenomics kmer split_kmers distance clustering | Calculate pairwise distances and basic clustering from SKA sketches |
| nf-core/ska/fasta | Process | genomics metagenomics kmer split_kmers sketch | Create genome sketch using split k-mers |
| nf-core/smudgeplot/all | Process | Smudgeplot reference-free kmer plots | Generating smudgeplot k-mer inference plots |
| nf-core/smudgeplot/hetmers | Process | Smudgeplot reference-free kmer ploidy genomics | Inference of ploidy and heterozygosity structure using whole genome sequencing data using FASTK databases |
| nf-core/sourmash/compare | Process | compare FracMinHash sketch containment sourmash metagenomics genomics kmer | Compare many FracMinHash signatures generated by sourmash sketch. |
| nf-core/sourmash/gather | Process | FracMinHash sketch signature kmer containment sourmash genomics metagenomics taxonomic classification taxonomic profiling | Search a metagenome sourmash signature against one or many reference databases and return the minimum set of genomes that contain the k-mers in the metagenome. |
| nf-core/sourmash/index | Process | signatures sourmash genomics metagenomics mapping kmer | Create a database of sourmash signatures (a group of FracMinHash sketches) to be used as references. |
| nf-core/sourmash/pairwise | Process | compare |