A simple example is provided as follows to illustrate the use of "LWFQZip2". To compress the sample FASTQ file SRR1063349.fastq, the command "LWFQZip2 -c" is executed with a reference NC_017634.1.fasta.

LWFQZip2 -c -i SRR1063349.fastq -r NC_017634.1.fasta

where the target FASTQ file is first mapped to the reference obtaining an intermediate output file "SRR1063349.fastq.map.txt"(in SAM format) in the same directory, and then the original data is compressed based on this mapping results. A compressed file "SRR1063349.fastq.lz" is obtained.

To decompress the file, the command "LWFQZip2 -d" should be called.

LWFQZip2 -d -i SRR1063349.fastq.lz -r NC_017634.1.fasta

More parameters can be specified for the mapping and compressiong parts as follows:

COMMANDS AND OPTIONS

LWFQZip2	<mode>...[options]
	Mode:
	-c compression. -d decompression.
	Compression/Decompression Options:
	-i input FASTQ file or compressed file. -r input Reference file. -m maximal read length,ranging from 30000 to 300000 (Default: '-m 300000'). -h help. -g best compression ratio mode (slow), usage: LWFQZip2 -c -i input -r reference -g. -a assemble-based mode,An optional amount (Default: 0.3% of the original file size) of reads, which contains the predefined prefix (Default: 'CG'), could be combined to be an artificial reference. At the end of the package, this artificial reference is included. usage: LWFQZip2 -c -i input.fastq -a 0.003(default) LWFQZip2 -d -i input.fastq.lz -a. -s display the counts of the common prefixes in the reference, e.g. CG,AT,ATA... -v version.
	Mapping Options:
	-b the number of mapping thread(Default: 10, mininum: 1) -p specify the kmer prefixes, e.g.,'CG', 'AT', and 'TAG' (Default: '-p CG'). 'AA' is not recommended as a prefix. -k length of a kmer used in locate local alignment. (Default: '-k 8'). -l the mini length of a legal alignment.(Default: '-l 12'). -o the complementary palindrome mode.(Default: '-o 1' means start,otherwise'-o 0'). -e the tolerance rate of mismatches.(Default: '-e 0.05').