Transrate
Description
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.
Licencs
MIT License. Transrate is research software. We therefore require that users cite Transrate if they use it in a publication.
Usage
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/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
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
Documentation
http://hibberdlab.com/transrate/getting_started.html