Workflows
What is a Workflow?Filters
Query
Created At
Updated At
Tool
Bakta1
BEDTools1
BioPerl1
Biopython1
Clair31
Filtlong1
Flye1
FreeBayes1
Liftoff1
LongReadSum1
Minimap21
QUAST1
SAMtools1
snpEff1
More...
Workflow type
Common Workflow Language2
Tag
Bioinformatics2
CWL2
plasmids2
Annotation1
Assembly1
Galaxy1
genbank1
Genomics1
gff31
plasmid1
Python1
Workflows1
More...
Submitter
Martijn Melissen2
Space
Independent Teams2
Creator
Martijn Melissen2
Scientific disciplines
Agricultural and Biological Sciences2
Maturity
Stable2
2
Workflows visible to you, out of a total of 2
Stable
Workflow for long read quality control, contamination filtering, assembly, variant calling and annotation.
- Preprocessing of reference file
- LongReadSum before and after filtering (read quality control)
- Filtlong filter on quality and length
- Flye assembly
- Minimap2 mapping of reads and assembly
- Clair3 variant calling of reads
- Freebayes variant calling of assembly
- Optional Bakta annotation of genomes with no reference
- SnpEff building or downloading of a database
- SnpEff functional ...
Stable
Workflow for preprocessing the reference file. Downloads the GenBank file from NCBI if not provided, concatenates plasmid GenBank file(s) with each other and the reference file, extracts GFF3 from the (merged) reference.
This workflow on WorkflowHub: https://workflowhub.eu/workflows/1818
All tool CWL files and other workflows can be found here: Tools: https://git.wur.nl/ssb/automated-data-analysis/cwl/-/tree/main/tools Workflows: https://git.wur.nl/ssb/automated-data-analysis/cwl/-/tree/main/workflows ...
