KMC
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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
For accessing k-mers stored in database produced by KMC there is an API (kmc_api directory). Note that for KMC versions 0.x and 1.x dababase format differs from produced by KMC version 2.x. From version 2.2.0 API is unified for both formats and all new features/bug fixes are present only for 2.x branch (standalone API for older KMC version is not longer under development, so new version of API should be used even for databases produced by older KMC version).
Installation
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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 kmer_counter/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/)
Note: asmlib is free only for non commercial purposes. If needed, you can contact the author of asmlib or compile KMC without asmlib.
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.
If you want to compile kmc without asmlib run:
make DISABLE_ASMLIB=true
#####Additional infromation for MAC OS installation
For compilation under MAC OS there is makefile_mac.
Usage:
make -f makefile_mac
There might be a need to change g++ path in makefile_mac.
If needed we recommend install g++ with brew (http://brew.sh/).
Note that KMC creates a hundreds of temporary files, while default limit for opened files is small for under MAC OS platform.
To increase this number use following command before running KMC:
ulimit -n 2048
Directory structure
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* bin - 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
Binaries
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After compilation you will obtain two binaries:
* bin/kmc - the main program for counting k-mer occurrences
* bin/kmc_dump - the program listing k-mers in a database produced by kmc
License
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* KMC software distributed under GNU GPL 2 licence.
* libbzip2 is open-source (BSD-style license)
* gzip is free, open-source
* asmlib is under the licence GNU GPL 3 or higher
Note: for commercial usage of asmlib follow the instructions in 'License conditions' (http://www.agner.org/optimize/asmlib-instructions.pdf) or compile KMC without asmlib.
In case of doubt, please consult the original documentations.
Warranty
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE,
TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING
THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.