Transfuse

Transfuse

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 perform your transcriptome assembly and a list of your assemblies as fasta files and produces a single output fasta file.

Installation and Running

Download the latest release and unpack it. This package contains everything that transfuse needs including a version of ruby.

Usage

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

  -a, --assemblies=<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)
  -i, --id=<f>            sequence identity to cluster at (default: 1.0)
  -v, --verbose           be verbose
  -e, --version           Print version and exit
  -h, --help              Show this message

An example command:

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

Contributing

Tranfuse is currently in development.

If you want to suggest, and maybe implement, a new feature, please suggest it on the tracker first.

License

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

Transfuse is released under the MIT license.