Workflows
What is a Workflow?Filters
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
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
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 ...
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
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 ...
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 ...
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 ...
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 ...
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
Combined workflow for large genome assembly
The tutorial document for this workflow is here: https://doi.org/10.5281/zenodo.5655813
What it does: A workflow for genome assembly, containing subworkflows:
- Data QC
- Kmer counting
- Trim and filter reads
- Assembly with Flye
- Assembly polishing
- Assess genome quality
Inputs:
- long reads and short reads in fastq format
- reference genome for Quast
Outputs:
- Data information - QC, kmers
- Filtered, trimmed reads
- Genome assembly, assembly graph, ...