Nextflow Modules
Showing module(s) with keyword "search"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/blat | Process | blat sequence search | Queries a sequence subject |
| nf-core/entrezdirect/esearch | Process | public datasets entrez search ncbi database | Searches a term in a public NCBI database |
| nf-core/entrezdirect/xtract | Process | public datasets entrez search ncbi database | Queries an NCBI database using an UID |
| nf-core/fasta_explore_search_plot_tidk | Workflow | genomics telomere repeat search plot | Uses Telomere Identification toolKit (TIDK) to identify the frequency of telomeric repeats along a sliding window for each sequence in the input fasta file. Results are presented in TSV and SVG formats. The user can specify an a priori sequence for identification. Possible a posteriori sequences are also explored and the most frequent sequence is used for identification similar to the a priori sequence. seqkit/seq and seqkit/sort modules are also included to filter out small sequences and sort sequences by length. |
| nf-core/fasta_hmmsearch_rank_fastas | Workflow | hmmer search rank fasta | Run hmmsearch and output separate fasta files for top scoring hits to each profile |
| nf-core/hmmer/hmmbuild | Process | search hidden Markov model HMM hmmer hmmsearch | create an hmm profile from a multiple sequence alignment |
| nf-core/macsyfinder/search | Process | genomics protein macromolecular systems hmmer search | Search for macromolecular systems in protein datasets using MacSyFinder |
| nf-core/ripgrep | Process | search regex patterns | ripgrep recursively searches directories for a regex pattern |
| nf-core/skani/search | Process | skani metagenomics genome alignment search | Memory-efficient ANI database queries with skani. |
| nf-core/tidk/explore | Process | genomics telomere search | `tidk explore` attempts to find the simple telomeric repeat unit in the genome provided. It will report this repeat in its canonical form (e.g. TTAGG -> AACCT). |
| nf-core/tidk/plot | Process | genomics telomere search plot | Plots telomeric repeat frequency against sliding window location using data produced by `tidk/search` |
| nf-core/tidk/search | Process | genomics telomere search | Searches a genome for a telomere string such as TTAGGG |