Workflows

What is a Workflow?
43 Workflows visible to you, out of a total of 43

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, ...

Type: Galaxy

Creator: Luke Silver

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.881.4

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 ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.880.1

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 ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.879.1

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, ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.878.1

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 ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.877.1

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 ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.876.1

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 = masked_genome.fasta and table of repeats found.

...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.875.2

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. New default settings for BUSCO: lineage = eukaryota; for Quast: lineage = eukaryotes, genome = large. Reports assembly stats into a table called metrics.tsv, including selected metrics from Fasta Stats, and read coverage; reports BUSCO versions and dependencies; and displays these tables in the workflow ...

Type: Galaxy

Creators: Gareth Price, Anna Syme

Submitter: Johan Gustafsson

Work-in-progress

ONTViSc (ONT-based Viral Screening for Biosecurity)

Introduction

eresearchqut/ontvisc is a Nextflow-based bioinformatics pipeline designed to help diagnostics of viruses and viroid pathogens for biosecurity. It takes fastq files generated from either amplicon or whole-genome sequencing using Oxford Nanopore Technologies as input.

The pipeline can either: 1) perform a direct search on the sequenced reads, 2) generate clusters, 3) assemble the reads to generate longer contigs or 4) directly ...

Type: Nextflow

Creators: Marie-Emilie Gauthier, Craig Windell, Magdalena Antczak, Roberto Barrero

Submitter: Magdalena Antczak

DOI: 10.48546/workflowhub.workflow.683.1

Stable

 

Welcome to the pipesnake. Let's get started.


Introduction

pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity ...

Type: Nextflow

Creators: Ziad Al-Bkhetan, Ian Brennan

Submitter: Ziad Al-Bkhetan

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