README

This sofware implements a parallel Locality-Sensitive Hashing based heuristic algorithm to construct overlap graphs for large genomic datasets.

Dependencies

• A modern, C++11 ready compiler such as g++ version 4.7 or higher or clang version 3.2 or higher.
• The cmake build system (Version >= 2.8.11).
• A 64-bit Linux system.
• An MPI implementation. Tested with OpenMPI and MPICH only.

Compilation

bruno/bliss librares are included as a submodules under the directory ext/bliss. Initialize the submodules as below, if they are not already initialized.

git submodule init
git submodule update

bruno/bliss also depends upon mxx and google sparse hash, we initialize them as follows

cd ext/bliss
git submodule init
git submodule update
cd ../../

A bug in bruno is causes a error for compilation. So, we apply a patch on bruno/bliss as follows

patch -p0 < bliss.patch

Now, we are read to build the executable. First, compile google's sparshash so that the header files are configured properly.

cd ext/bliss/ext/sparshash
./configure
make
cd ../../../../

Next, create a build directory outside of the source directory. For example,

 mkdir build
 cd build

Finally, build the executable find_seq_overlaps as follows.

 cmake ../
 make

Usage of the executbale

The name of the executable is find_seq_overlaps. Input files are provided in the FASTQ format. Input arguments are providede as follows:

find_seq_overlaps  [-R <string>] [-C <string>] [-r <unsigned>] [-k
                    <int>] [-M <int>] [-T <int>] [-B <int>] [-d <int>]
                    [-O <string>] [-p <string>] -t <string> [--]
                    [--version] [-h] <file_names> ...

Where:

-R <string>,  --true_file <string>
  File with true pairs

-C <string>,  --candidate_file <string>
  File with candidate pairs

-r <unsigned>,  --read_length <unsigned>
  read length

-k <int>,  --kmer_length <int>
  Kmer Length

-M <int>,  --max_bucket_size <int>
  Max Bucket Size

-T <int>,  --block_size <int>
  Block Size

-B <int>,  --block_count <int>
  Number of blocks

-d <int>,  --overlap_threshold <int>
  Minimum Overlap

-O <string>,  --output_prefix <string>
  Prefix for output files, including directory

-p <string>,  --position_file <string>
  Position for input file (full path)

-t <string>,  --run_type <string>
  (required)  Type of run : One of 'candidate', 'true', 'eval' 

--,  --ignore_rest
  Ignores the rest of the labeled arguments following this flag.

--version
  Displays version information and exits.

-h,  --help
  Displays usage information and exits.

<string>  (accepted multiple times)
  FASTA or FASTQ file names