Workflows

What is a Workflow?
36 Workflows visible to you, out of a total of 36
Stable

Fastq-to-BAM @ NCI-Gadi is a genome alignment workflow that takes raw FASTQ files, aligns them to a reference genome and outputs analysis ready BAM files. This workflow is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes on NCI Gadi to run all stages of the workflow in parallel, either massively parallel using the scatter-gather approach or parallel by sample. It consists of a number of stages and follows the BROAD Institute's best practice ...

Type: Shell Script

Creators: Cali Willet, Tracy Chew, Georgina Samaha, Rosemarie Sadsad, Andrey Bliznyuk, Ben Menadue, Rika Kobayashi, Matthew Downton, Yue Sun

Submitter: Georgina Samaha

DOI: 10.48546/workflowhub.workflow.146.1

workflow-partial-gstacks-populations

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

This workflow takes in bam files and a population map.

To generate bam files see: https://workflowhub.eu/workflows/351

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

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

Shotgun Metagenomics Analysis

Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more

Description

The input for this analysis is paired end next generation sequencing data from metagenomic samples. The workflow is designed to be modular, so that individual modules can be run depending on the nature of the metagenomics project at hand. More modules will be added as we develop them - this repo is a work in progress!

These scripts have been written ...

Type: Shell Script

Creators: Cali Willet, Rosemarie Sadsad, Tracy Chew, Smitha Sukumar, Elena Martinez, Christina Adler, Henry Lydecker, Fang Wang

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.327.1

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