Workflows
What is a Workflow?Filters
MGnify's amplicon pipeline v5.0. Including the Quality control for single-end and paired-end reads, rRNA-prediction, and ITS sub-WFs.
Type: Galaxy
Creators: Rand Zoabi, Paul Zierep, EMBL's European Bioinformatics Institute
Submitter: WorkflowHub Bot
Classification and visualization of ITS regions.
Type: Galaxy
Creators: Rand Zoabi, Paul Zierep, EMBL's European Bioinformatics Institute
Submitter: WorkflowHub Bot
Quality control subworkflow for paired-end reads.
Type: Galaxy
Creators: Rand Zoabi, Paul Zierep, EMBL's European Bioinformatics Institute
Submitter: WorkflowHub Bot
Quality control subworkflow for single-end reads.
Classification and visualization of SSU, LSU sequences.
Type: Galaxy
Creators: Rand Zoabi, Paul Zierep, EMBL's European Bioinformatics Institute
Submitter: WorkflowHub Bot
This workflow creates taxonomic summary tables out of the amplicon pipeline results.
Contiging Solo:
Generate assembly based on PacBio Hifi Reads.
Inputs
- Hifi long reads [fastq]
- K-mer database [meryldb]
- Genome profile summary generated by Genomescope [txt]
- Homozygous Read Coverage. Optional, use if you think the estimation from Genomescope is inacurate.
- Genomescope Model Parameters generated by Genomescope [tabular]
- Database for busco lineage (recommended: latest)
- Busco lineage (recommended: vertebrata)
- Name of first assembly
- Name of second ...
The workflow takes trimmed HiC paired-end reads collection, and Pri/Alt assemblies to produce a scaffolded primary assembliy (and alternate contigs) using YaHS. It also runs all the QC analyses (gfastats, BUSCO, and Merqury).
Calculate extended gamma-ray source halo using crbeam simulation