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

DESCRIPTION:
Analyse 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 http://hibberdlab.com/transrate

USAGE:
transrate <options>

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