minirmd is a tool to remove duplicate reads. The program is written in C++11 (tested with g++ >= 5.4.0) and works on Linux.
git clone https://github.com/yuansliu/minirmd.git
cd minirmd
make
conda install -c bioconda minirmd
sh runtest.sh
./minirmd -i test.fastq -o test_rm_1.fastq -d 1
./minirmd -i test_1.fastq -f test_2.fastq -o test_rm_2.fastq -d 2
Parameters
-i reads file, a FASTQ file
-f reads file, a FASTQ file; if paired-end
-o the output file
Options
-d number of allowed mismatch; default is 0
-k the file to sotre values of k
-r remove duplicates on reverse-complement strand
-t number of threads (default 24)
-h print help message
For the following fastq format file, the second "header123" will be ignored by the tool.
@header123
CGTATGCTACGTAC
+header123
KKKKKIIKKKKIII
If any bugs, please email to yyuanshengliu@gmail.com