rnabridge-denovo implements an efficient algorithm to bridge paired-end RNA-seq reads, i.e., to find the sequences of full fragments given the sequences of paired-end reads. Its sister tool, rnabridge-align, determines the alignments of full fragments given the alignments of paired-end reads. See rnabridge-test for the evaluation of both tools.
rnabridge-denovo uses additional library Bifrost for de Bruijn graph construction, the instrcution for downloading and installing Bifrost is here(https://github.com/pmelsted/bifrost).
If you add the option -DCMAKE_INSTALL_PREFIX=/pathtobifrost to the cmake command in building Bifrost, the install path for Bifrost will not be the default path. Remember to set the environment variables C_INCLUDE_PATH, CPLUS_INCLUDE_PATH, LD_LIBRARY_PATH, LIBRARY_PATH and PATH correctly.
export C_INCLUDE_PATH=$C_INCLUDE_PATH:/pathtobifrost/include/
export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:/pathtobifrostinclude/
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/pathtobifrost/lib/
export LIBRARY_PATH=$LIBRARY_PATH:/pathtobifrost/lib/
export PATH=$PATH:/pathtobifrost/lib/
Use the following to compile rnabridge-align:
cd src
make
The usage of rnabridge-denovo is:
./rnabridge-denovo pathtoread1.fq pathtoread2.fq pathtooutputbridge.fa
pathtoread1.fq and pathtoread2.fq are your input paired-end RNA-seq reads. pathtooutputbridge.fa is the path for the output file, which contains all the brdiges in fasta format.