Workflows

What is a Workflow?
736 Workflows visible to you, out of a total of 791

workflow-partial-bwa-mem

These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the tools from the Stacks program.

Galaxy Australia: https://usegalaxy.org.au/

Stacks: http://catchenlab.life.illinois.edu/stacks/

This workflow is part of the reference-guided stacks workflow, https://workflowhub.eu/workflows/347

Inputs

  • demultiplexed reads in fastq format, may be output from the QC workflow. Files are in a collection.
  • reference genome in fasta format ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

workflow-partial-cstacks-sstacks-gstacks

These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the tools from the Stacks program.

Galaxy Australia: https://usegalaxy.org.au/

Stacks: http://catchenlab.life.illinois.edu/stacks/

This workflow takes in ustacks output, and runs cstacks, sstacks and gstacks.

To generate ustacks output see https://workflowhub.eu/workflows/349

For the full de novo workflow see https://workflowhub.eu/workflows/348

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

workflow-partial-ustacks-only

These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the tools from the Stacks program.

Galaxy Australia: https://usegalaxy.org.au/

Stacks: http://catchenlab.life.illinois.edu/stacks/

For the full de novo workflow see https://workflowhub.eu/workflows/348

You may want to run ustacks with different batches of samples.

  • To be able to combine these later, there are some necessary steps - we need to keep track of how many ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

workflow-denovo-stacks

These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the tools from the Stacks program.

Galaxy Australia: https://usegalaxy.org.au/

Stacks: http://catchenlab.life.illinois.edu/stacks/

Inputs

  • demultiplexed reads in fastq format, may be output from the QC workflow. Files are in a collection.
  • population map in text format

Steps and outputs

ustacks:

  • input reads go to ustacks.
  • ustacks assembles the reads into matching ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

workflow-ref-guided-stacks

These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the tools from the Stacks program.

Galaxy Australia: https://usegalaxy.org.au/

Stacks: http://catchenlab.life.illinois.edu/stacks/

Inputs

  • demultiplexed reads in fastq format, may be output from the QC workflow. Files are in a collection.
  • population map in text format
  • reference genome in fasta format

Steps and outputs

BWA MEM 2:

  • The reads are mapped to the ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

workflow-qc-of-radseq-reads

These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the tools from the Stacks program.

Galaxy Australia: https://usegalaxy.org.au/

Stacks: http://catchenlab.life.illinois.edu/stacks/

Inputs

  • demultiplexed reads in fastq format, in a collection
  • two adapter sequences in fasta format, for input into cutadapt

Steps and outputs

The workflow can be modified to suit your own parameters.

The workflow steps are:

  • Run ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

Work-in-progress

A workflow for the quality assessment of mass spectrometry (MS) based proteomics analyses

Objective. Biomarkers have become important for the prognosis and diagnosis of various diseases. High-throughput methods such as RNA-sequencing facilitate the detection of differentially expressed genes (DEGs), hence potential biomarker candidates. Individual studies suggest long lists of DEGs, hampering the identification of clinically relevant ones. Concerning preeclampsia, a major obstetric burden with high risk for adverse maternal and/or neonatal outcomes, limitations in diagnosis and ...

Type: Galaxy

Creator: Marlene Rezk

Submitter: Marlene Rezk

DOI: 10.48546/workflowhub.workflow.338.1

ESCALIBUR

Escalibur Population Genomic Analysis Pipeline is able to explore key aspects centering the population genetics of organisms, and automates three key bioinformatic components in population genomic analysis using Workflow Definition Language (WDL: https://openwdl.org/), and customised R, Perl, Python and Unix shell scripts. Associated programs are packaged into a platform independent singularity image, for which the definition file is provided.

The workflow for analysis using Escalibur ...

Type: Workflow Description Language

Creators: None

Submitter: Pasi Korhonen

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