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
• Convert formats
• Fgenesh annotation (this workflow)

Inputs Required

Files uploaded by the user:

• assembled_genome.fasta — the assembled genome
• hard_masked_genome.fasta — hard repeat-masked genome
• mRNA_sequences.fasta — known mRNAs in Fgenesh header format (typically the output of the upstream "Convert formats" workflow). Optional — see "Running without mRNA" below.

Selected at runtime (dropdowns / tick-boxes, not uploads):

• Closely-related species (Fgenesh species matrix, from those installed on Galaxy Australia)
• Mammal or non-mammal
• NR database (for Fgenesh get proteins)
• BUSCO lineage
• Licence agreement (tick to accept Fgenesh terms)

Running without mRNA

If no known mRNA sequences are available, edit the Fgenesh-annotate step's mRNA option to "no" and disconnect the mRNA input.

Processing Steps

Splits the input genomes into single sequences (to reduce runtime), annotates each with Fgenesh++, and merges the outputs.

Outputs

• Genome annotation (GFF3)
• Annotation stats
• FASTA files of mRNAs, cDNAs and proteins
• BUSCO report of proteins

Key Note

The sequences passed to the mRNA/cDNA extraction tools are the unmasked assembly; there may be situations where the masked version is preferable.