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 Use GCC to build

cd 

####Modified YASS for group hits A prebuild excecuteble file can found under /yass/cmake-build-debug

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 ####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