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Transrate #
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Structured data


Transrate: #

Software for de-novo transcriptome assembly quality analysis. - Genome Res.2016.

Overview #

  • by inspecting the contig sequences
  • by mapping reads to the contigs and inspecting the alignments
  • by aligning the contigs against proteins or transcripts from a related species and inspecting

command-line interface #

Transrate v1.0.3 by Richard Smith-Unna, Chris Boursnell, Rob Patro, Julian Hibberd, and Steve Kelly

DESCRIPTION: Analyze a de-novo transcriptome assembly using three kinds of metrics:

1. sequence based (if --assembly is given)
2. read mapping based (if --left and --right are given)
3. reference based (if --reference is given)

Documentation at

  • USAGE: transrate


  • --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 [read, ref, all]
  • --examples: Show some example commands with explanations