minirmd

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.

Download & Compile

git clone https://github.com/yuansliu/minirmd.git
cd minirmd
make

Install from bioconda

conda install -c bioconda minirmd

Test

sh runtest.sh

Usage

./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

Note

For the following fastq format file, the second "header123" will be ignored by the tool.

@header123
CGTATGCTACGTAC
+header123
KKKKKIIKKKKIII

Contacts

If any bugs, please email to yyuanshengliu@gmail.com