Minicom is a tool for compressing short reads in FASTQ. The minicom program is written in C++11 and works on Linux. It is availble under an open-source license.
git clone https://github.com/yuansliu/minicom.git
cd minicom
sh install.sh
In the script install.sh, it downloads the tools bsc and p7zip. Please make sure the two tools can be ran on your machine.
As "alloca" is used in the source code. It needs more stack memory. Plase check the stack size before running minicom using the comman ulimit -s. If it is very small, please change it by ulimit -s unlimited. We are grateful to Prof. Sebastian Deorowicz for reporting the bug.
To compress:
./minicom -r IN.fastq
./minicom -r IN.fastq -p #order-preserving mode
./minicom -1 IN_1.fastq -2 IN_2.fastq #preserving paired-end information
Minicom creates compressed file IN_comp.minicom, IN_comp_order.minicom and IN_comp_pe.minicom respectively.
Options for compression
-h print help message
-t number of threads, default: 24
-r reads file
-1 reads file of paired-end reads [used for paired-end]
-2 reads file of paired-end reads [used for paired-end]
-k length of k-mer, k <= 31, default: 31
-e difference threshold, default: 4
-m number of minimizer, default 6
-w window size, default L/2-k, where L is the length of reads
-s number of indexed substring, default L/17 for L > 80; otherwise L/11
-S step size of threshold, default S = e
-E maximum threshold, default L/2
-p order-preserving mode [only used for compressing single FASTQ file]
To decompress:
./minicom -d IN.minicom [-t number of threads, default 24]
Yuansheng Liu, Zuguo Yu, Marcel E. Dinger, Jinyan Li; Index suffix-prefix overlaps by (w, k)-minimizer to generate long contigs for reads compression. Bioinformatics, 2018. https://doi.org/10.1093/bioinformatics/bty936.
If any bugs during you run our code, please email to [email protected]