SLAM-Seq indexer and aligner

SLAM-Seq aligner is a Burrows–Wheeler transform (BWT) based fast indexer/aligner specialized in allow specific T to C mismatch in some constant ratio and parallelized searching for Next Generation Sequencing data.

SLAM-Seq aligner 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 SLAM-Seq aligner.

Run the binary directly without installation

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

bin/FSU_searcher 		# for linux
bin/FSU_indexer 		# for linux

Get the latest version of the software

git clone [email protected]:jhhung/SLAM-Seq-Aligner.git

Compile the software by typing:

make

##USAGE

See help

FSU_searcher --help
FSU_indexer --help

Build genomic index (similar to bowtie-build)

FSU_indexer --input_file [genome.fa] --output_file [ouput prefix]

Mapping

FSU_searcher --input_file [reads.fq] --index_file [index prefix] --allow_mismatch --thread_number [thread number]

##Contact

• Jui-Hung Hung [email protected]
• Chia-Hua Chang [email protected]
• Chiung-Po Hsiao [email protected]