Workflows
What is a Workflow?Filters
Query
Created At
Updated At
Tool
Binette1
BUSCO1
CheckM1
eggNOG1
Flye1
Hostile1
InterProScan (EBI)1
KofamKOALA1
kofamscan1
kraken21
MaxBin1
MetaBAT 21
Minimap21
NanoPlot1
QUAST1
SemiBin1
Sequali1
SPAdes1
More...
Workflow type
Common Workflow Language2
Tag
illumina2
Assembly1
binning1
Classification1
filtering1
Genomics1
Metagenomics1
quality1
Transcriptomics1
More...
Submitter
Bart Nijsse2
Team
UNLOCK2
Space
Independent Teams2
Topic annotations
Bioinformatics1
Data quality management1
Metagenomic sequencing1
Metagenomics1
Sequence assembly1
2
Workflows visible to you, out of a total of 2
Work-in-progress
Workflow (hybrid) metagenomic assembly and binning
- Workflow Illumina Quality:
- Sequali (control)
- hostile contamination filter
- fastp (quality trimming)
- Workflow Longread Quality:
- NanoPlot (control)
- fastplong (quality trimming)
- hostile contamination filter
- Kraken2 taxonomic classification of FASTQ reads
- SPAdes/Flye (Assembly)
- Medaka/PyPolCA (Assembly polishing)
- QUAST (Assembly quality report)
(optional)
- Workflow binnning
- Metabat2/MaxBin2/SemiBin
- Binette
- BUSCO
...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Changlin Ke
Submitter: Bart Nijsse
Stable
Workflow for Illumina Quality Control and Filtering
Multiple paired datasets will be merged into single paired dataset.
Summary:
- FastQC on raw data files
- fastp for read quality trimming
- BBduk for phiX and (optional) rRNA filtering
- Kraken2 for taxonomic classification of reads (optional)
- BBmap for (contamination) filtering using given references (optional)
- FastQC on filtered (merged) data
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Changlin Ke
Submitter: Bart Nijsse
