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, virAnnot pipeline, Ay Lab, iPC: individualizedPaediatricCure, Harkany Lab, Genomics Coordination Center, EJPRD WP13 case-studies workflows, Common Workflow Language (CWL) community, Testing, SeBiMER, IAA-CSIC, MAB - ATGC
Web page: Not specified
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)
DownloadWorkflow for NonSpliced RNAseq data with multiple aligners.
Steps: - workflowquality.cwl: - FastQC (control) - fastp (trimming) - bowtie2 (read mapping) - samto_sorted-bam - featurecounts (transcript read counts) - kallisto (transcript [pseudo]counts)
Amplicon analysis workflow using NG-Tax
Steps:
- Quality control on the reads
- Execute NGTax for ASV detection and classification
For more information about NG-Tax 2.0 have a look at https://doi.org/10.3389/fgene.2019.01366
Type: Common Workflow Language
Creators: Jasper Koehorst, Bart Nijsse, Jesse van Dam, Peter Schaap,
Submitter: Jasper Koehorst
Workflow for (paired) read quality control, trimming and contamination filtering based on a given reference.
Will output a merged set of read pairs, when multiple datasets are used.
Steps:
FastQC (read quality control)
fastp (read quality trimming)
bbduk used (rrna filtering)
bbmap (contamination filter)
Workflow for Metagenomics from raw reads to bins.
Steps:
workflow_quality.cwl:
FastQC (control)
fastp (quality trimming)
bbmap contamination filter
SPAdes (Assembly)
QUAST (Assembly quality report)
BBmap (Read mapping to assembly)
MetaBat2 (binning)
CheckM (bin completeness and contamination)
GTDB-Tk (bin taxonomic classification)
