Workflows

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68 Workflows visible to you, out of a total of 70

Stable

Amplicon analysis workflow using NG-Tax

Type: Common Workflow Language

Creators: Jasper Koehorst, Jesse van Dam, Bart Nijsse, Peter Schaap,

Submitter: Jasper Koehorst

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)

Type: Common Workflow Language

Creators: None

Submitter: Bart Nijsse

Work-in-progress

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)

Type: Common Workflow Language

Creators: None

Submitter: Jasper Koehorst

Work-in-progress

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

Creators: None

Submitter: Bart Nijsse

Stable

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

Type: Unrecognized workflow type

Creators: Carlos Oscar Sorzano Sanchez, Roberto Melero, Marta Martinez

Submitter: Laura del Cano

Stable

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.

Type: Unrecognized workflow type

Creators: None

Submitter: Carlos Oscar Sorzano Sanchez

Work-in-progress

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

...

Type: Galaxy

Creators: None

Submitter: Matteo Chiara

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