Nextflow Modules
Showing module(s) with keyword "bacteria"
| Module | Keywords | Description |
|---|---|---|
| nf-core/abricate/run | bacteria assembly antimicrobial resistance | Screen assemblies for antimicrobial resistance against multiple databases |
| nf-core/abricate/summary | bacteria assembly antimicrobial reistance | Screen assemblies for antimicrobial resistance against multiple databases |
| nf-core/abritamr/run | bacteria fasta antibiotic resistance | A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes |
| nf-core/amrfinderplus/run | bacteria fasta antibiotic resistance | Identify antimicrobial resistance in gene or protein sequences |
| nf-core/amrfinderplus/update | bacteria fasta antibiotic resistance | Identify antimicrobial resistance in gene or protein sequences |
| nf-core/antismash/antismash | secondary metabolites BGC biosynthetic gene cluster genome mining NRPS RiPP antibiotics prokaryotes bacteria eukaryotes fungi antismash | antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. |
| nf-core/antismash/antismashdownloaddatabases | 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/antismashlite | secondary metabolites BGC biosynthetic gene cluster genome mining NRPS RiPP antibiotics prokaryotes bacteria eukaryotes fungi antismash | antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. |
| nf-core/antismash/antismashlitedownloaddatabases | 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/bakta | annotation fasta bacteria | Annotation of bacterial genomes (isolates, MAGs) and plasmids |
| nf-core/bakta/baktadbdownload | bakta annotation fasta bacteria database download | Downloads BAKTA database from Zenodo |
| nf-core/deepbgc/download | database download BGC biosynthetic gene cluster deep learning neural network random forest genomes bacteria fungi | Database download module for DeepBGC which detects BGCs in bacterial and fungal genomes using deep learning. |
| nf-core/deepbgc/pipeline | BGC biosynthetic gene cluster deep learning neural network random forest genomes bacteria fungi | DeepBGC detects BGCs in bacterial and fungal genomes using deep learning. |
| nf-core/gapseq/doall | metabolic model gap filling pathway prediction bacteria genome-scale model complete workflow | Complete gapseq workflow from genome to gap-filled model |
| nf-core/gapseq/draft | metabolic model draft reconstruction bacteria genome-scale model | Create draft metabolic model from pathway and transporter predictions |
| nf-core/gapseq/fill | metabolic model gap filling bacteria genome-scale model | Perform gap filling on draft metabolic model |
| nf-core/gapseq/find | metabolic pathways genomics bacteria pathway prediction | Predict metabolic pathways from genomic data using gapseq |
| nf-core/gapseq/findtransport | transporters genomics bacteria transporter prediction | Predict transporters from genomic data using gapseq |
| nf-core/gtdbtk/classifywf | GTDB taxonomy taxonomic classification metagenomics classification genome taxonomy database bacteria archaea | GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. |
| nf-core/gtdbtk/gtdbtoncbimajorityvote | gtdb taxonomy ncbi taxonomy taxonomic classification conversion taxonomy classification genome taxonomy database bacteria archaea | Converts the output classifications of GTDB-TK from GTDB taxonomy to NCBI taxonomy |