An open infrastructure for exploring new horizons for research on microbial communities.
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:
- FastQC (Read Quality Control)
- fastp (Read Trimming)
- STAR (Read mapping)
- featurecounts (transcript read counts)
- kallisto (transcript [pseudo]counts)
Workflow 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
- 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
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.
FastQC (read quality control)
fastp (read quality trimming)
bbduk used (rrna filtering)
bbmap (contamination filter)
Workflow for Metagenomics from raw reads to bins.
fastp (quality trimming)
bbmap contamination filter
QUAST (Assembly quality report)
BBmap (Read mapping to assembly)
CheckM (bin completeness and contamination)
GTDB-Tk (bin taxonomic classification)