Workflows
What is a Workflow?Filters
This workflow
- Reconstruct phylogeny (insert fragments in a reference)
- Alpha rarefaction analysis
- Taxonomic analysis
Type: Galaxy
Creators: Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZ
Submitter: WorkflowHub Bot
Nanopore datasets analysis - Phylogenetic Identification - antibiotic resistance genes detection and contigs building
Microbiome - QC and Contamination Filtering
Pathogens of all samples report generation and visualization
Microbiome - Taxonomy Profiling
This workflow takes a collection of BAM (output of STAR) and a gtf. It extends the input gtf using de novo annotation.
Annotation of an assembled bacterial genomes to detect genes, potential plasmids, integrons and Insertion sequence (IS) elements.
Type: Galaxy
Creators: ABRomics , Pierre Marin, Clea Siguret, abromics-consortium
Submitter: WorkflowHub Bot
Antimicrobial resistance gene detection from assembled bacterial genomes
Type: Galaxy
Creators: ABRomics , Pierre Marin, Clea Siguret, abromics-consortium
Submitter: WorkflowHub Bot
Importing single-end multiplexed data (not demultiplexed yet)
Type: Galaxy
Creators: Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZ
Submitter: WorkflowHub Bot
Use DADA2 for sequence quality control. DADA2 is a pipeline for detecting and correcting (where possible) Illumina amplicon sequence data. As implemented in the q2-dada2 plugin, this quality control process will additionally filter any phiX reads (commonly present in marker gene Illumina sequence data) that are identified in the sequencing data, and will filter chimeric sequences.
Type: Galaxy
Creators: Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZ
Submitter: WorkflowHub Bot