Applications/Transrate

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

Next Steps

• http://hibberdlab.com/transrate/index.html

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