GroupK is an overlap detection tool for DNA sequnces from PacBio.
Here is the old code for the experiment. The C++ implementation will be released soon
- Python 3 (You may need to modify some script if you want to use Python 2.7)
- CMake 3.7 or higher
- GCC 4.8 or higher
- Biopython library for Python
- SortedContainers library fot Python
At this stage, our tool consists three part:
A prebuild excecuteble file using GCC 4.8.2 can found under /sa_filter/
Use GCC 4.8 or higher to build
cd sa_filter
g++ -std=c++11 *.cpp -o filter
To excecute (although this will be included in the script)
./filter -i <infile> -k <kmersize> -o <outfile>
The program will do all against all to compare shared kmer
A prebuild excecuteble file using GCC 4.8.2 can found under /yass/
And to use CMake to build under Linux
cd yass
cmake -G "Unix Makefiles"
make
After finished build, you can use the python script to excecute it to get output of groups of given fasta files
The output format is (seperated by tab)
query_id, query length, target_id, target_length, groups(x, diagonal, length)
To run GroupK, after build the two program above
cd script
python GroupK.py [-h] [--k1 K1] [--threshold THRESHOLD] [--k2 K2]
[--accuracy ACCURACY] [--gap GAP] [--chain CHAIN]
[--groupc GROUPC] [--idbase IDBASE] [--ratio RATIO]
[--size SIZE] [--large LARGE]
input output
positional arguments:
input path of input fasta file
output path of output file
optional arguments:
-h, --help show this help message and exit
--k1 K1 kmer size for filtration (default: 15)
--threshold THRESHOLD
count threshold for shared k1 (default: 2)
--k2 K2 kmer size for group (default: 9)
--accuracy ACCURACY accuracy of the reads (default: 0.85)
--gap GAP gap rate (default: 0.12)
--chain CHAIN number of kmer in the chain to report (default: 3)
--groupc GROUPC the coefficeint c in paper to control chaining
threshold, must be non-zero float (default: 4.0)
--idbase IDBASE if the number of identical base meet this threshold
the final chain threshold will be release by the --large times (default: 400)
--ratio RATIO ratio of two overlap region threshold (default: 0.5)
--size SIZE group size threshold (default: 12)
--large LARGE release threhold for large overlap (default: 2)
Right now, the main bottle neck is the yass part.
how to cite this tool:
Du N., Chen J., Sun Y., Improving the sensitivity of detecting long read overlaps using grouped short k-mer matches, accepted to APBC 2019