A highly hardware-acceleration friendly k-ordered FM-index for exact string matching, overlap graph construction for de novo assembly, and more.

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.


*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

Get the latest version of the software

git clone

Enter the folder sBWT and:

cmake .

Compile the software by typing:





Build genomic index (similar to bowtie-build)

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


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

GPU version


In sbwtCuda direction

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

Compile from the source code

Install the dependencies

Enter the folder sbwtCuda and:

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.