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: ...

ORBiT

A Nextflow workflow for analysing Oxford Nanopore Technologies (ONT) RNAseq direct read sequening (DRS) or cDNA data.

This workflow emphasises sensitivity to detect rare and novel features within the data. Multiple aspects of this workflow are tailored to enhance sensitivity:

• Alignment to reference genome rather than transcriptome
• Multiple tools per analysis type (n = 2 isoforms, n = 3 fusions)
• Reads quantification tools capable of detecting novel isoforms, and counting at the isoform ...

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 ...

scRNAvigator: Interactive exploration, processing, and analysis of your scRNA-seq data

This collection of R notebooks has been designed to guide you through processing and analysing your single cell RNA (scRNA) sequencing data. They are designed to be worked through in the following order:

1. Quality control
2. Doublet detection
3. Dataset integration
4. Cell annotation
5. Pseudobulking and differential gene expression analysis
6. Pathway enrichment analyses.

Each notebook explains what is ...

Somatic-ShortV @ NCI-Gadi is a variant calling pipeline that calls somatic short variants (SNPs and indels) from tumour and matched normal BAM files following GATK's Best Practice Workflow. 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. ...

Germline-ShortV @ NCI-Gadi is an implementation of the BROAD Institute's best practice workflow for germline short variant discovery. This implementation is optimised for the National Compute Infrastucture's Gadi HPC, utilising scatter-gather parallelism to enable use of multiple nodes with high CPU or memory efficiency. This workflow requires sample BAM files, which can be generated using the Fastq-to-bam @ NCI-Gadi pipeline. Germline-ShortV can be applied ...

Bootstrapping-for-BQSR @ NCI-Gadi is a pipeline for bootstrapping a variant resource to enable GATK base quality score recalibration (BQSR) for non-model organisms that lack a publicly available variant resource. This implementation is optimised for the National Compute Infrastucture's Gadi HPC. Multiple rounds of bootstrapping can be performed. Users can use Fastq-to-bam @ NCI-Gadi and Germline-ShortV @ NCI-Gadi to ...