Transrate

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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.

Category

Annotation

Availability

Version 1.0.3

Licence

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

Use

module add transrate-1.0.3
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

Homepage

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

Program manager

meta@cesnet.cz