Fig. 1
From: LW-FQZip 2: a parallelized reference-based compression of FASTQ files
The general framework of LW-FQZip 2. Firstly, the input FASTQ file is split into three data streams of metadata, bases, and quality scores. Secondly, the quality scores and metadata are compacted with run-length-limited encoding and incremental encoding, respectively. The nucleotide bases are partitioned and mapped to an external reference sequence based on the light-weight mapping model. Finally, the processed intermediate files from the three streams are compressed with arithmetic coder and/or other specific coding schemes