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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.


MIT License. Transrate is research software. We therefore require that users cite Transrate if they use it in a publication.


Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/

to your script before loading a module. Then, you can list all versions of transrate and load default version of transrate as

module avail transrate/ # list available modules
module load transrate   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail transrate

and choose explicit version you want to use.

transrate --assembly input.fasta -o output
--assembly             Assembly file(s) in FASTA format, comma-separated
--left                 Left reads file(s) in FASTQ format, comma-separated
--right                Right reads file(s) in FASTQ format, comma-separated
--reference            Reference proteome or transcriptome file in FASTA format
--threads              Number of threads to use (default: 8)
--merge-assemblies     Merge best contigs from multiple assemblies into file
--output               Directory where results are output (will be created) (default: transrate_results)
--loglevel             Log level. One of [error, info, warn, debug] (default: info)
--install-deps         Install any missing dependencies. One of [ref]
--examples             Show some example commands with explanations