/bin/bash -c "$(curl -fsSL"

Some features require htslib 1.10+ and Python 3.5+. If you want to use Python interop, you also need to point SEQ_PYTHON to the Python library (typically called or similar). Also, if you have a custom build of htslib, you can point SEQ_HTSLIB to it (e.g. export SEQ_HTSLIB=/path/to/


Assuming that Seq was properly installed, you can use it as follows:

seqc file.seq  # Compile and run file.seq
seqc -d file.seq  # Compile and run file.seq in debug mode
seqc -o file.bc file.seq  # Compile file.seq to LLVM bytecode file file.bc

It is highly recommended to use -d parameter for development purposes: compilation is faster, stack traces are actually useful, and it has some extra checks (e.g. null checks) that can save your life.

Creating a stand-alone executable

Currently, stand-alone executables must be created manually:

seqc -o prog.bc prog.seq
llc prog.bc -filetype=obj -o prog.o
clang -L/path/to/libseqrt/ -lseqrt -lomp -ldl -pthread -o prog prog.o

You might need to install LLVM to use llc. Seq uses LLVM 6, so we advise against using older versions. /path/to/libseqrt/ would typically be $HOME/.seq/lib/seq.

If you want to be able to easily distribute your executable, pass -Wl,-rpath,\$ORIGIN to clang and ship the and in the same directory with your executable. This is a Linux-specific argument; on macOS you might want to use -Wl,-rpath,"@loader_path" instead.