Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Picrust 2 - Export module for ngtax
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)
Workflow to build different indices for different tools from a genome and transcriptome.
This workflow expects an (annotated) genome in GBOL ttl format.
Steps: - SAPP: rdf2gtf (genome fasta) - SAPP: rdf2fasta (transcripts fasta) - STAR index (Optional for Eukaryotic origin) - bowtie2 index - kallisto index
Type: Common Workflow Language
Submitter: Bart Nijsse