A java package for filtering of sequencing reads. Only reads with D2R value higher than the threshold will be kept.
- Usage:
java -jar D2RReadFilter \path\to\read\fasta\file kmersize threshold pt pc pg pa
Example:
java -jar D2RReadFilter.jar reads.fa 7 0.00015 17 34 34 17
A genome scanner spotting highly repetitive regions on genome. The program is written in C++ with Visual Studio 2017. Only standard libraries are used in the single cpp code file. You can remove the #include "stdafx.h" line in the front of D2R_codes/D2RGenomeScanner/D2Rscanner/D2Rscanner.cpp to compile it with other compilers or IDEs.
- Usage:
Build it as an executable file
D2Rscannerand run it
D2Rscanner \path\to\genome\fasta\file window_size kmer_size
Example:
D2Rscanner E:\code\D2R\CRISPR\genomes\NC_010162.fa 1000 7
A python library for hacking.
Written in swig, supporting Win64 and Linux64 environment currently.
Copy files under release_win_x64 or release_linux_x64 to your working directory and
import pyd2r, D2R function is available with def D2R_nNorm(seq, k, pt, pc, pg, pa)