A highly hardware-acceleration friendly k-ordered FM-index for exact string matching, overlap graph construction for de novo assembly, and more.
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.
*Only 64 bits systems are able to compile and run sBWT aligner.
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
git clone git@github.com:jhhung/sBWT.git
$BOOST_ROOT
to the directory of boost if CMake cannot find boost automatically;$CC
and $CXX
to the gcc/g++ compiler you want to use.cmake .
make
make
sbwt build -i [genome.fa] -p [ouput prefix]
sbwt map -i [reads.fq] -p [index prefix] -o [output.sam]
In sbwtCuda direction
bin/com_rf #for mapping
bin/com_tbl #for indexing
$CC
and $CXX
to the gcc/g++ compiler you want to use.make com_rf #for mapping
make com_tbl #for indexing
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.