Nextflow Modules
Showing module(s) with keyword "database"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/antismash/antismashdownloaddatabases | Process | secondary metabolites BGC biosynthetic gene cluster genome mining NRPS RiPP antibiotics prokaryotes bacteria eukaryotes fungi antismash database | antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases for conda and docker/singularity runs. |
| nf-core/antismash/antismashlitedownloaddatabases | Process | secondary metabolites BGC biosynthetic gene cluster genome mining NRPS RiPP antibiotics prokaryotes bacteria eukaryotes fungi antismash database | antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases for conda and docker/singularity runs. |
| nf-core/bakta/baktadbdownload | Process | bakta annotation fasta bacteria database download | Downloads BAKTA database from Zenodo |
| nf-core/bigslice/downloaddb | Process | biosynthetic gene clusters genomics database download | Downloads and extracts the BiG-SLiCE HMM database (biosynthetic and sub Pfams) using the bundled `download_bigslice_hmmdb` script shipped with BiG-SLiCE. The resulting directory can be passed directly as the `hmmdb` input to the `BIGSLICE` module. |
| nf-core/blast/blastdbcmd | Process | fasta blast database retrieval identifier | Retrieve entries from a BLAST database |
| nf-core/blast/makeblastdb | Process | fasta blast database | Builds a BLAST database |
| nf-core/blast/updateblastdb | Process | fasta blast download database | Downloads a BLAST database from NCBI |
| nf-core/bracken/build | Process | kraken2 bracken database build | Extends a Kraken2 database to be compatible with Bracken |
| nf-core/catpack/download | Process | taxonomic classification classification database download | Downloads the required files for either Nr or GTDB for building into a CAT database |
| nf-core/catpack/prepare | Process | catpack cat prepare database profiling build | Creates a CAT_pack database based on input FASTAs |
| nf-core/centrifuge/build | Process | database metagenomics build db fasta | Build centrifuge database for taxonomic profiling |
| nf-core/checkv/downloaddatabase | Process | checkv checkm mag metagenome quality isolates virus completeness contamination download database | Construct the database necessary for checkv's quality assessment |
| nf-core/deeparg/downloaddata | Process | download database deeparg antimicrobial resistance genes deep learning prediction | A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes |
| nf-core/deepbgc/download | Process | database download BGC biosynthetic gene cluster deep learning neural network |