Workflows

Amplicon analysis workflow using NG-Tax

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 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)

• SAPP (bin annotation)

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

Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures

Scipion is a workflow engine mostly for Cryo-Electron Microscopy image processing. In this extremely simple workflow, we load the Relion 3.0 tutorial data and process it to 2.9A resolution.

This WF is based on the official Covid19-Galaxy assembly workflow as available from https://covid19.galaxyproject.org/genomics/2-assembly/ . It has been adapted to suit the needs of the analysis of metagenomics sequencing data. Prior to be submitted to INDSC databases, these data need to be cleaned from contaminant reads, including reads of possible human origin.

The assembly of the SARS-CoV-2 genome is performed using both the Unicycler and the SPAdes assemblers, similar to the original WV.

To

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