Leon

Linux	Mac OSX	Functional tests

What is Leon?

Leon is a software to compress Next Generation Sequencing data. It can compress Fasta or Fastq format; plain text and gzipped files are supported.

The method does not require any reference genome, instead a reference is built de novo from the set of reads as a probabilist de Bruijn Graph. It uses the disk streaming k-mer counting algorithm contained in the GATB-Core library, and inserts solid k-mers in a bloom-filter. Each read is then encoded as a path in this graph, storing only an anchoring kmer and a list of bifurcations indicating which path to follow in the graph if several are possible.

G. Benoit, C. Lemaitre, D. Lavenier, E. Drezen, T. Dayris, R. Uricaru, G. Rizk. (2015) Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph. BMC Bioinformatics, 2015, 16:288.

Getting the latest source code

Requirements

CMake 3.1+; see http://www.cmake.org/cmake/resources/software.html

c++/11 compiler; compilation was tested with gcc and g++ version>=4.8 (Linux) and clang version>=3.6 (Mac OSX).

Instructions

# get a local copy of source code
git clone --recursive https://github.com/GATB/leon.git

# compile the code an run a simple test on your computer
cd leon
sh INSTALL

MANUAL

Usage

Mandatory options:

-file  (1 arg) :    input file (e.g. FASTA/FASTQ for compression or .leon file for decompression)  
-c             :    compress  
-d             :    decompress

Optional parameters:

-nb-cores: number of cores 
(default is the maximum available number of cores)

Optional Compression parameters:

-kmer-size <int>  :    kmer size  (default 31), currently should be <32 (or need to recompile, see below)
-abundance <int>  :    minimal abundance threshold for solid kmers  (default: automatic)
-lossless         :    switch to lossless compression for qualities (default is lossy. lossy has much higher compression rate, and the loss is in fact a gain. lossy is better!)
-seq-only         :    store dna sequence only, header and qualitiess are discarded, will decompress to fasta (same as -noheader -noqual)
-noheader         :    discard header
-noqual           :    discard quality scores

Examples :

leon -file data/toy.fasta -c 
   -> generates the file toy.leon

leon -file toy.leon  -d 
   -> "restores" the file toy.fasta

Note:

In order to use k values larger than 31, recompilation is necessary.

In the sequence of commands given in the INSTALL file, change the command:

cmake ..

cmake -Dk1=64 -Dk2=96 -Dk3=128 -Dk4=162 ..

this will allow to use k<63. For larger k, change the values such that they are multiple of 32 and k1<k2<k3<k4.

CHANGELOG

version 1.1.0: July 13, 2017:
- Leon compressor integrated into GATB-Core 1.4.0, main source code is now included in GATB-Core source code
- Leon compressed data is now stored into a single HDF5 binary file: '.leon'
- bug fixes on compression/decompression of very small reads
- Extensive test suite added; read more
- Leon now successfully works on the data sets reported as breaking Leon in Y. Zhang et al, 2017
version 1.0.0: April 16, 2015: bug fixes
version 0.3: March 19, 2015 added quality compression, and other optimizations
version 0.2.1: Dec 18, 2014: bug fixes
version 0.2: Oct 31, 2014: major performance improvement (about ~ 2 times faster)
version 0.1.2 Aug 10, 2014: initial public release

Contact

To contact a developer, request help, etc: https://gatb.inria.fr/contact/

ysard / leon