GroupK

GroupK is a overlap detection tool for DNA sequnces from PacBio.

Usage

• 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

Usage

At this stage, our tool consists three part: ####Suffix array filter 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

####Modified YASS for group hits 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)

####Python script

References

how to cite this tool:

Du N., Chen J., Sun Y., Improve the sensitivity of detecting long read overlaps using grouped short k-mer matches, submitted to ISMB 2018