enamcse / kmc

kmc

KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files. The homepage of the KMC project is http://sun.aei.polsl.pl/kmc

Instalation

Before compilation you need to install some libraries and modify makefile.

The necessary libraries that should be installed on a computer are:

• Boost version 1.51 or higher (for Boost/filesystem and Boost/thread libraries) change BOOST_LIB and BOOST_H in makefile to the directories where Boost is installed.

The following libraries come with KMC in a binary (64-bit compiled for x86 platform) form. If your system needs other binary formats, you should put the following libraries in src/kmc/libs:

• asmlib - for fast memcpy operation (http://www.agner.org/optimize/asmlib-instructions.pdf)
• libbzip2 - for support for bzip2-compressed input FASTQ/FASTA files (http://www.bzip.org/)
• zlib - for support for gzip-compressed input FASTQ/FASTA files (http://www.zlib.net/)

If needed, you can also redefine maximal length of k-mer, which is 256 in the current version. Note: KMC is highly optimized and spends only as many bytes for k-mer (rounded up to 8) as necessary, so using large values of MAX_K does not affect the KMC performance for short k-mers.

Some parts of KMC use C++11 features, so you need a compatible C++ compiler, e.g., gcc 4.7 or higher.

After that, you can run make to compile kmc and kmc_dump applications.

Directory structure

. - main directory of KMC (programs after compilation will be stored here) kmer_counter - source code of kmc program kmer_counter/libs - compiled binary versions of libraries used by KMC kmc_api - C++ source codes implementing API; must be used by any program that wants to process databases produced by kmc kmc_dump - source codes of kmc_dump program listing k-mers in databases produced by kmc