Workflow Type: Galaxy
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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, the additional inputs required are .cdna, .pro and .dat files.
What it does:
- This workflow splits the input genomes into single sequences (to decrease computation time), annotates using FgenesH++, and merges the output.
Outputs:
- genome annotation in gff3 format
- fasta files of mRNAs, cDNAs and proteins
- Busco report
Steps
ID | Name | Description |
---|---|---|
0 | assembled_genome.fasta | fgenesh_split |
1 | repeat_masked_genome.fasta | fgenesh_split |
2 | FGENESH annotate | fgenesh_annotate |
3 | Merge into a single annotation file | fgenesh_merge |
4 | FGENESH merge | fgenesh_merge |
5 | FGENESH get mRNA or GC | fgenesh_get_mrnas_gc |
6 | FGENESH get mRNA or GC | fgenesh_get_mrnas_gc |
7 | FGENESH get protein | fgenesh_get_proteins |
8 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
Version History
Version 2.2 (latest) Created 18th Jun 2024 at 10:46 by Anna Syme
Adding .ga file
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Version-2.2
76451e8
Version 2.1 Created 18th Jun 2024 at 10:08 by Anna Syme
add updated workflow image
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Version-2.1
3cebff9
Version 1 (earliest) Created 8th May 2024 at 08:28 by Anna Syme
Initial commit
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Version-1
1b30a7e
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Creator
Submitter
Tool
Citation
Silver, L. (2024). Fgenesh annotation -TSI. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.881.4
Activity
Views: 1523 Downloads: 269 Runs: 0
Created: 8th May 2024 at 08:28
Last updated: 18th Jun 2024 at 09:59
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