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 3 (latest) Created 17th Nov 2024 at 23:41 by Anna Syme
Changes made 13 Nov 2024: Added correct input files and connected them to the split steps. Added inputs for db selections in the annotation step. Added lineage input to Busco. Added genome annotation stats derived from gff3 output. Connected in assembly.fasta sequences to "get mRNA/cDNA" tools. Expanded this information text and clarified the need for .cdna .pro and .dat files as input.
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Version 2.1 Created 18th Jun 2024 at 10:08 by Anna Syme
add updated workflow image
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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: 17th Nov 2024 at 23:51
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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.
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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
