UNLOCK
OverviewAn open infrastructure for exploring new horizons for research on microbial communities.
Space: Independent Teams
SEEK ID: https://workflowhub.eu/projects/16
Public web page: https://m-unlock.nl
Organisms: No Organisms specified
WorkflowHub PALs: No PALs for this Team
Team start date: 1st Sep 2020
Related items
https://orcid.org/0000-0001-8172-8981
Work-in-progress
Workflow for Metagenomics from raw reads to annotated bins.
Steps:
workflow_quality.cwl:
FastQC (control)
fastp (trimming)
Kraken2 (Taxonomic Read Classification
SPAdes (Assembly)
QUAST (Assembly quality report)
BBmap (Read mapping to assembly)
samtobam (sam to indexed bam)
metabatContigDepths (jgisummarizebamcontigdepths)
MetaBat2 (binning)
Download
Work-in-progress
Workflow for read quality control and trimming.
Steps:
FastQC (read quality control)
fastp (read quality trimming)
bbduk used for rrna filtering
Work-in-progress
Workflow for NonSpliced RNAseq data with multiple aligners.
Steps:
workflow_quality.cwl:
FastQC (control)
fastp (trimming)
bowtie2 (read mapping)
samtosorted-bam
featurecounts (transcript read counts)
kallisto (transcript [pseudo]counts)
Work-in-progress
Workflow for Spliced RNAseq data
Steps:
workflow_quality.cwl:
FastQC (Read Quality Control)
fastp (Read Trimming)
STAR (Read mapping)
featurecounts (transcript read counts)
kallisto (transcript [pseudo]counts)
Stable
Amplicon analysis workflow using NG-Tax
Type: Common Workflow Language
Creators: Jasper Koehorst, Jesse van Dam, Bart Nijsse, Peter Schaap,
Submitter: Jasper Koehorst
