This repository provides programs for the k-mer analysis to detect unintended external DNA in a host genome.
Move to the directory of the k-mer analysis programs and type make.
First of all, install Homebrew. See the following page for installation.
Next, install llvm.
brew install llvm
In the directory of the k-mer analysis programs, just type make. If you don't have make in your computer, you also have to install it.
There are two programs. The first one is countmer that counts the numbers of the k-mers.
./countmer vector.fasta mutant_read1.fastq.gz mutant_read2.fastq.gz kmer mutant > mutant.out
./countmer vector.fasta wildtype_read1.fastq.gz wildtype_read2.fastq.gz kmer wildtype > wildtype.out
The input files and options to be specified are as follows:
vector.fasta: Vector sequence (FASTA format)
read1.fastq.gz: R1 (forward) read
read2.fastq.gz: R2 (reverse) read
kmer: # of k (This value must be 16 or more and 20 is recommended)
mutant/wildtype: Names used as a prefix of output files
*.out: The total # of the k-mers, which is used in the second program.
The second program is gtest that conducts a G-test.
./gtest mutant.posFreq.txt wildtype.posFreq.txt #mutantMers #wildtypeMers out_prefix
The command line options are:
mutant.posFreq.txt: An output file of countmer
wildtype.posFreq.txt: An output file of countmer
#mutantMers: The number written in mutant.out
#wildtypeMers: The number written in wildtype.out
out_prefix is a string used as a prefix of an output file.
The output file is out_prefix.result and its contents are: position on the vector, k-mer count in mutant, k-mer count in wild type, G statistic with Williams collection, and * (if G > 6.634).