A FASTQ compressor based on integer-mapped k-mer indexing for biologist

• An integer-mapped k-mer indexing method was applied to NGS sequence data compression.
• KIC, a user-friendly FASTQ compressor, was developed and thoroughly tested.
• The KIC method showed the highest compression ratio for FASTQ sequence data.
• KIC's overall performance is comparable to the latest dedicated compression tools.
• KIC has demonstrated outstanding reliability, user-friendliness, and compatibility.

Next generation sequencing (NGS) technologies have gained considerable popularity among biologists. For example, RNA-seq, which provides both genomic and functional information, has been widely used by recent functional and evolutionary studies, especially in non-model organisms. However, storing and transmitting these large data sets (primarily in FASTQ format) have become genuine challenges, especially for biologists with little informatics experience. Data compression is thus a necessity. KIC, a FASTQ compressor based on a new integer-mapped k-mer indexing method, was developed (available at http://www.ysunlab.org/kic.jsp). It offers high compression ratio on sequence data, outstanding user-friendliness with graphic user interfaces, and proven reliability. Evaluated on multiple large RNA-seq data sets from both human and plants, it was found that the compression ratio of KIC had exceeded all major generic compressors, and was comparable to those of the latest dedicated compressors. KIC enables researchers with minimal informatics training to take advantage of the latest sequence compression technologies, easily manage large FASTQ data sets, and reduce storage and transmission cost.