Workflows
What is a Workflow?Filters
Query
Created At
Updated At
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
Maturity
Work-in-progress1
2
Workflows visible to you, out of a total of 2
Work-in-progress
Workflow for long read quality control, contamination filtering, assembly, variant calling and annotation.
Steps:
- Preprocessing of reference file : https://workflowhub.eu/workflows/1818
- 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 ...
**Workflow for preprocessing a reference file. **
Steps: -When a GenBank file is not provided, it is downloaded from NCBI based on a accession number. -When multiple plasmid GenBank files are provided, they are merged into one file. -When any amount of plasmid GenBank files are provided, the reference is merged with the plasmid GenBank file(s) into one file. A FASTA file is also extracted. -When no plasmid Genbank files are provided, a FASTA file is extracted from the reference GenBank file. -A ...
