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
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, Australian BioCommons, virAnnot pipeline, Ay Lab
Web page: Not specified
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
Workflow for read quality control and trimming.
Steps:
FastQC (read quality control)
fastp (read quality trimming)
bbduk used for rrna filtering
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)
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)
Amplicon analysis workflow using NG-Tax
Type: Common Workflow Language
Creators: Jasper Koehorst, Jesse van Dam, Bart Nijsse, Peter Schaap,
Submitter: Jasper Koehorst
