Transfuse

Transfuse is currently in development and is not yet ready for use

Transfuse intelligently merges your multiple de novo transcriptome assemblies. Run multiple assemblies with different de novo assemblers, or different settings in the same assembler and have them combined into a single high quality transcriptome.

Transfuse takes in the reads you used to do the assembly and a list of fasta files and produces a single output fasta file.

Installation and Running

To install Transfuse, clone this repo:

git clone https://github.com/cboursnell/transfuse.git

Then build and install the ruby gem

gem build *spec; gem install *gem

Usage

Transfuse is run on the command line. The options are:

  -a, --assembly=<s>    assembly files in FASTA format, comma-separated
  -l, --left=<s>        left reads file in FASTQ format
  -r, --right=<s>       right reads file in FASTQ format
  -o, --output=<s>      write merged assembly to file
  -t, --threads=<i>     number of threads (default: 1)
  -v, --verbose         be verbose
  -e, --version         Print version and exit
  -h, --help            Show this message

An example command:

transfuse --assembly soap-k31.fa,soap-k41.fa,soap-k51.fa --left reads_1.fq --right reads_2.fq --output soap-merged.fa --threads 12

License

This is adademic software - please cite us if you use it in your work.

Transfuse is released under the MIT license.