Difference between revisions of "Applications/Transrate"
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==Usage== | ==Usage== | ||
| − | Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly. | + | Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, and reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly. |
===Example=== | ===Example=== | ||
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You can examine your contigs without using the reads or a reference. All you need is the assembly in FASTA format. | You can examine your contigs without using the reads or a reference. All you need is the assembly in FASTA format. | ||
| − | For example if you have the assembly in the file '''transcripts.fa''': | + | For example, if you have the assembly in the file '''transcripts.fa''': |
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| − | == | + | ==Next Steps== |
* [http://hibberdlab.com/transrate/index.html http://hibberdlab.com/transrate/index.html] | * [http://hibberdlab.com/transrate/index.html http://hibberdlab.com/transrate/index.html] | ||
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Latest revision as of 11:00, 16 November 2022
Application Details
- Description: Transrate is software for de-novo transcriptome assembly quality analysis.
- Version: 1.0.3
- Modules: transrate/1.0.3
- Licence: Free, open-source
Usage
Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, and reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.
Example
You can examine your contigs without using the reads or a reference. All you need is the assembly in FASTA format.
For example, if you have the assembly in the file transcripts.fa:
[username@login]$ module add transrate/1.0.3 [username@login]$ transrate --assembly transcripts.fa