sBWT indexer and aligner

sBWT is a Burrows–Wheeler transform (BWT) based fast indexer/aligner specialized in parallelized indexing and searching for Next Generation Sequencing data.

sBWT is released under GPLv2 with additional restriction so that is only applicable to individuals and non-profits and that any for-profit company must purchase a different license.

##INSTALL *Only 64 bits systems are able to compile and run sBWT aligner.

Run the binary directly without installation

Please try the precompiled binaries first, most of the linux systems should be able to run Tailor without any troubles.

bin/sbwt_linux 		# for linux

Compile from the source code

Install the dependencies

• 1.1 Relative recent C++ compiler that support most features of C++11. We recommend GCC.
• 1.2 Boost
• 1.3 CMake

Get the latest version of the software

git clone git@github.com:jhhung/sBWT.git

Enter the folder sBWT and:

• Set environmental variable $BOOST_ROOT to the directory of boost if CMake cannot find boost automatically;
• Set environmental variable $CC and $CXX to the gcc/g++ compiler you want to use.

cmake .

Compile the software by typing:

make

troubleshooting

• If you got linker error, it is possible that the default library in the lib/ is not suitable to your platform. There are one librarie for linux available, rename the file that fit the best to "libabwt_table.a", and retype

make

##USAGE

Build genomic index (similar to bowtie-build)

sbwt build -i [genome.fa] -p [ouput prefix]

Mapping

sbwt map -i [reads.fq] -p [index prefix] -o [output.sam]

GPU version

##Install In sbwtCuda direction

bin/com_rf	#for mapping
bin/com_tbl	#for indexing

Compile from the source code

Install the dependencies

• 1.1 Relative recent C++ compiler that support most features of C++11. We recommend GCC.
• 1.2 Boost
• 1.3 CUDA's Compute Capability 2.0, Tesla K20 is recommended

Enter the folder sbwtCuda and:

• Set environmental variable $CC and $CXX to the gcc/g++ compiler you want to use.

make com_rf		#for mapping
make com_tbl	#for indexing

##USAGE

com_tbl [reference.fa] xxx 3125 128 4000000					#for indexing
#the bwt file will generate in local diretion where you run the program.

com_rf xxx [reads.fq] 3125 128 [reads number] > [output.sam] 	#for mapping
#the "xxx" and numeric parameter is unessesery please just copy it.

##Contact

• Jui-Hung Hung juihunghung@gmail.com
• Min-Te Chou poi5305@gmail.com
• Ting-Wei Hong thestyle1202@gmail.com
• Chia-Hua Chang CHChang810716@gmail.com