MPXV (Mpox) Phylogenetic Analysis with Squirrel

Description

Galaxy workflow to perform MPXV phylogenetic reconstruction using the Squirrel (Some QUIck Reconstruction to Resolve Evolutionary Links) Galaxy tools, Squirrel QC and Squirrel Phylo. The workflow also performs masking (using the squirrel tool) of SNPs.

Galaxy Squirrel tools:

• Squirrel QC: The quality control (QC) mode of Squirrel that can run QC on the alignment and flag certain sites ...

Viral Amplicon Analysis Pipeline for ONT Data

Description

Galaxy workflow for processing viral amplicon datasets, such as MPXV (Mpox), sequenced using the Oxford Nanopore Technologies (ONT) platform. The workflow uses the latest Fieldbioinformatics Artic Minion pipeline that uses the clair3 variant caller.

The ARTIC minion is a pipeline for working with viral nanopore sequencing data, generated from tiling amplicon schemes. It is designed ...

Note: Deprecated as of May 2025. The mRNA preprocessing previously performed by this workflow is now built into the Fgenesh annotation workflow (881) Version 4. This workflow is no longer needed in the TSI annotation pipeline. Please use workflow 881 Version 4 directly with TransDecoder CDS output from workflow 879 (Extract transcripts).

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, ...

Fgenesh Annotation - TSI Workflow Description

Overview

One of a series of workflows to annotate a genome, tagged TSI-annotation. Based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

Workflow Sequence

Run in this order:

• Repeat masking
• RNAseq QC and read trimming
• Find transcripts
• Combine transcripts
• Extract transcripts
• Fgenesh annotation (this workflow)

Inputs Required

Files uploaded by the user:

• assembled_genome.fasta — the ...

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

• What it does: Polishes (corrects) an assembly, using long reads (with the tools Racon and Medaka) and short reads (with the tool Racon). (Note: medaka is only for nanopore reads, not PacBio reads).
• Inputs: assembly to be polished: assembly.fasta; long reads - the same set used in the assembly (e.g. may be raw or filtered) fastq.gz format; short reads, R1 only, in fastq.gz format
• Outputs: ...

Post-genome assembly quality control workflow using Quast, BUSCO, Meryl, Merqury and Fasta Statistics, with updates November 2024.

Workflow inputs: reads as fastqsanger.gz (not fastq.gz), and primary assembly.fasta. (To change reads format: click on the pencil icon next to the file in the Galaxy history, then "Datatypes", then set "New type" as fastqsanger.gz). Note: the reads should be those that were used for the assembly (i.e., the filtered/cleaned reads), not the raw reads.

What it does: ...

Taxonomy Assignment with QIIME2

This workflow performs taxonomic assignment for an input OTU/ASV (Operating Taxonomic Unit/Amplicon Sequence Variant) Feature Table and set of amplicon Representative Sequences using QIIME2. The workflow creates and trains a QIIME2 classifier for an input reference taxonomic database (e.g. HOMD, SILVA, PR2, UNITE) and uses the trained classifier to assign taxonomy ...

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] ...

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, ...