The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.

Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.

• Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
• Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
• Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
• Scalable: Galaxy ...

Genome assembly workflow for nanopore reads, for TSI

Input:

• Nanopore reads (can be in format: fastq, fastq.gz, fastqsanger, or fastqsanger.gz)

Optional settings to specify when the workflow is run:

• [1] how many input files to split the original input into (to speed up the workflow). default = 0. example: set to 2000 to split a 60 GB read file into 2000 files of ~ 30 MB.
• [2] filtering: min average read quality score. default = 10
• [3] filtering: min read length. default = 200
• [4] ...

Post-genome assembly quality control workflow using Quast, BUSCO, Meryl, Merqury and Fasta Statistics. Updates November 2023.

• Inputs: reads as fastqsanger.gz (not fastq.gz), and assembly.fasta. (To change format: click on the pencil icon next to the file in the Galaxy history, then "Datatypes", then set "New type" as fastqsanger.gz).
• New default settings for BUSCO: lineage = eukaryota; for Quast: lineage = eukaryotes, genome = large.
• Reports assembly stats into a table called metrics.tsv, ...

Scaffolding using HiC data with YAHS

This workflow has been created from a Vertebrate Genomes Project (VGP) scaffolding workflow.

• For more information about the VGP project see https://galaxyproject.org/projects/vgp/.
• The scaffolding workflow is at https://dockstore.org/workflows/github.com/iwc-workflows/Scaffolding-HiC-VGP8/main:main?tab=info
• Please see that link for the workflow diagram.

Some minor changes have been made to better fit with TSI project data:

• optional inputs of SAK info ...

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

• Repeat masking
• RNAseq QC and read trimming
• Find transcripts
• Combine transcripts
• Extract transcripts
• Convert formats
• Fgenesh annotation

Workflow information:

• Input = genome.fasta.
• Outputs = soft_masked_genome.fasta, hard_masked_genome.fasta, ...

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

• Repeat masking
• RNAseq QC and read trimming
• Find transcripts
• Combine transcripts
• Extract transcripts
• Convert formats
• Fgenesh annotation

For this workflow:

Inputs:

• assembled-genome.fasta
• hard-repeat-masked-genome.fasta
• If using the mRNAs option, ...

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

• Repeat masking
• RNAseq QC and read trimming
• Find transcripts
• Combine transcripts
• Extract transcripts
• Convert formats
• Fgenesh annotation

About this workflow:

• Inputs: transdecoder-peptides.fasta, transdecoder-nucleotides.fasta
• Runs many steps ...

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

• Repeat masking
• RNAseq QC and read trimming
• Find transcripts
• Combine transcripts
• Extract transcripts
• Convert formats
• Fgenesh annotation

About this workflow:

• Input: merged_transcriptomes.fasta.
• Runs TransDecoder to produce longest_transcripts.fasta ...

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

• Repeat masking
• RNAseq QC and read trimming
• Find transcripts
• Combine transcripts
• Extract transcripts
• Convert formats
• Fgenesh annotation

About this workflow:

• Inputs: multiple transcriptome.gtfs from different tissues, genome.fasta, coding_seqs.fasta, ...

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

• Repeat masking
• RNAseq QC and read trimming
• Find transcripts
• Combine transcripts
• Extract transcripts
• Convert formats
• Fgenesh annotation

About this workflow:

• Run this workflow per tissue.
• Inputs: masked_genome.fasta and the trimmed RNAseq reads ...

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

• Repeat masking
• RNAseq QC and read trimming
• Find transcripts
• Combine transcripts
• Extract transcripts
• Convert formats
• Fgenesh annotation

About this workflow:

• Repeat this workflow separately for datasets from different tissues.
• Inputs = collections ...

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 ...

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, ...

Assess genome quality; can run alone or as part of a combined workflow for large genome assembly.

• What it does: Assesses the quality of the genome assembly: generate some statistics and determine if expected genes are present; align contigs to a reference genome.
• Inputs: polished assembly; reference_genome.fasta (e.g. of a closely-related species, if available).
• Outputs: Busco table of genes found; Quast HTML report, and link to Icarus contigs browser, showing contigs aligned to a reference ...

Assembly polishing subworkflow: Racon polishing with long reads

Inputs: long reads and assembly contigs

Workflow steps:

• minimap2 : long reads are mapped to assembly => overlaps.paf.
• overaps, long reads, assembly => Racon => polished assembly 1
• using polished assembly 1 as input; repeat minimap2 + racon => polished assembly 2
• using polished assembly 2 as input, repeat minimap2 + racon => polished assembly 3
• using polished assembly 3 as input, repeat minimap2 + racon => ...

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

• Repeat masking
• RNAseq QC and read trimming
• Find transcripts
• Combine transcripts
• Extract transcripts
• Convert formats
• Fgenesh annotation