Quality analysis and comparison of transcriptome assemblies.
- Development status
- Transcriptome assembly quality metrics
- Installation
- Usage
- Requirements
- Getting help
This software is in early development. Users should be aware that until the first release is made, features may change faster than the documentation is updated. Nevertheless, we welcome bug reports.
transrate implements a variety of established and new metrics. They are explained in detail on the wiki.
Assuming all the requirements are met (see below), you can install transrate very easily. Just run at the terminal:
gem install transrate
If you're new to linux/unix, there's a detailed tutorial for installing transrate with all the dependencies on my blog.
transrate --help will give you...
Transrate v0.0.10 by Richard Smith <[email protected]>
DESCRIPTION:
Analyse a de-novo transcriptome
assembly using three kinds of metrics:
1. contig-based
2. read-mapping
3. reference-based
Please make sure USEARCH, bowtie 2 and eXpress are installed
and in the PATH.
Bug reports and feature requests at:
http://github.com/blahah/transrate
USAGE:
transrate <options>
OPTIONS:
--assembly, -a <s>: assembly file in FASTA format
--reference, -r <s>: reference proteome file in FASTA format
--left, -l <s>: left reads file in FASTQ format
--right, -i <s>: right reads file in FASTQ format
--insertsize, -n <i>: mean insert size (default: 200)
--insertsd, -s <i>: insert size standard deviation (default: 50)
--threads, -t <i>: number of threads to use (default: 8)
--version, -v: Print version and exit
--help, -h: Show this message
If you don't include --left and --right read files, the read-mapping based analysis will be skipped. I recommend that you don't align all your reads - just a subset of 500,000 will give you a very good idea of the quality. You can get a subset by running (on a linux system):
head -2000000 left.fastq > left_500k.fastq
head -2000000 right.fastq > right_500k.fastq
FASTQ records are 4 lines long, so make sure you multiply the number of reads you want by 4, and be sure to run the same command on both the left and right read files.
transrate --assembly assembly.fasta \
--reference reference.fasta \
--left l.fq \
--right r.fq \
--threads 4
require 'transrate'
assembly = Transrate::Assembly.new(File.expand_path('assembly.fasta'))
reference = Transrate::Assembly.new(File.expand_path('reference.fasta'))
t = Transrate::Transrater.new(assembly, reference)
left = File.expand_path('left.fq')
right = File.expand_path('right.fq')
puts t.all_metrics(left, right)
puts t.assembly_scoreFirst, you'll need Ruby v1.9.3 or greater installed. You can check with:
ruby --version
If you don't have Ruby installed, or you need a higher version, I recommend using RVM as your Ruby Version Manager. To install RVM along with the latest Ruby, just run:
\curl -L https://get.rvm.io | bash -s stable
Your Ruby installation should come with RubyGems, the package manager for Ruby. You can check with:
gem --version
If you don't have it installed, I recommend installing the latest version of Ruby and RubyGems using the RVM instructions above (in the Requirements:Ruby section).
Usearch (http://drive5.com/usearch), Bowtie2 (https://sourceforge.net/projects/bowtie-bio/files/bowtie2) and eXpress (http://bio.math.berkeley.edu/eXpress/) must be installed and in your PATH. Additionally, the Usearch binary executable should be named usearch.
If you need help using transrate, please post to the forum here.
If you think you've found a bug, please post it to the issues list.