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.
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
Tranfuse is currently in development.
If you want to suggest, and maybe implement, a new feature, please suggest it on the tracker first.
This is adademic software - please cite us if you use it in your work.
Transfuse is released under the MIT license.