MultiTrans is a tool for transcripts assmebly, which formulated the transcripts assembly problem into a mixed integer linear programming.
C++, Python, and Gurobi are required to be installed.
To use the paired-end information of assembly graphs, BWA is also required to be installed.
**Assembly graph
python MultiTran.py -m 1 -g /path/to/assembly/graph/assembly_graph_with_scaffolds.gfa
**Splicing graph
python MultiTran.py -m 2 -g /path/to/splicing/graph/RawGraphs_/
--model (or -m) : 1 assembly graph, 2 splcing graph
--graph_file (or -g) : *.gfa file of assembly graph or directory of splicing graph
--out_dir (or -o): directory of output
--reads1 (or -r1) : paired-end reads
--reads2 (or -r2) : paired-end reads
--test (or -t): testing the software
--help (or -h): MultiTrans usage
python multiple_trans_analyze.py -t trans1.fa,trans2.fa,trans3.fa -o /out_dir/
--transcripts_file_list (or -t): list of transcriptome.fa separated by commas --out_dir (or -o): directory of output
Your comments, bug reports, and suggestions are very welcomed. They will help us to further improve MultiTrans. If you have any troubles running MultiTrans, please contact us (Email: zhaojin@mail.sdu.edu.cn).