Fgenesh annotation -TSI
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Run on GalaxyThis 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 | FGENESH split | fgenesh_split |
| 1 | FGENESH split | fgenesh_split |
| 2 | FGENESH annotate | fgenesh_annotate |
| 3 | FGENESH merge | 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-2.276451e8
Version 2.1 Created 18th Jun 2024 at 10:08 by Anna Syme
add updated workflow image
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Version-2.1
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Version 1 (earliest) Created 8th May 2024 at 08:28 by Anna Syme
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Created: 8th May 2024 at 08:28
Last updated: 18th Jun 2024 at 09:59
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https://orcid.org/0000-0002-9906-0673
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Teams: Australian BioCommons, QCIF Bioinformatics, Pawsey Supercomputing Research Centre, Sydney Informatics Hub, Janis, Melbourne Data Analytics Platform (MDAP), Galaxy Australia
Web page: https://www.biocommons.org.au/
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Space: Australian BioCommons
Public web page: https://www.biocommons.org.au/
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
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Space: Australian BioCommons
Public web page: https://usegalaxy.org.au/
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
