Nextflow Modules
Showing module(s) with keyword "kmer"
| Module | Keywords | Description |
|---|---|---|
| nf-core/cobiontid/kmercounter | 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 | 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/mashmap | mapper aligner minhash kmer | Mashmap is an approximate long read or contig mapper based on Jaccard similarity |
| nf-core/merquryfk/ploidyplot | kmer smudgeplot ploidy | An improved version of Smudgeplot using FastK |
| nf-core/merqury/hapmers | genomics quality check qc kmer | A script to generate hap-mer dbs for trios |
| nf-core/metacache/build | genomics metagenomics taxonomy short reads long reads kmer k-mer metacache build reference | Taxonomic profiling database building with MetaCache |
| nf-core/ska/distance | genomics metagenomics kmer split_kmers distance clustering | Calculate pairwise distances and basic clustering from SKA sketches |
| nf-core/ska/fasta | genomics metagenomics kmer split_kmers sketch | Create genome sketch using split k-mers |
| nf-core/sourmash/compare | compare FracMinHash sketch containment sourmash metagenomics genomics kmer | Compare many FracMinHash signatures generated by sourmash sketch. |
| nf-core/sourmash/gather | 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 | 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/sketch | hash sketch sourmash genomics metagenomics taxonomic classification taxonomic profiling kmer | Create a signature (a group of FracMinHash sketches) of a sequence using sourmash |
| nf-core/sourmash/taxannotate | fracminhash sketch signature kmer containment sourmash genomics metagenomics taxonomic classification taxonomic profiling | Annotate list of metagenome members (based on sourmash signature matches) with taxonomic information. |
| nf-core/yak/count | kmer fastq sequence count assembly | a tool to build k-mer hash table for fasta and fastq files |