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.
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