title: A FASTQ compressor based on integer-mapped k-mer indexing for biologist.
abstract: 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.
authors.affiliation: Department of Research, Synblex LLC, State College, PA 16801, USA. Electronic address: yetingzhang@synblex.com.
authors.forename: Yeting
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: New Jersey Center for Science Technology and Mathematics, Kean University, Union, NJ 07083, USA. Electronic address: patkhyat@kean.edu.
authors.forename: Khyati
authors.initials: K
authors.lastname: Patel
authors.affiliation: New Jersey Center for Science Technology and Mathematics, Kean University, Union, NJ 07083, USA. Electronic address: endrawit@kean.edu.
authors.forename: Tony
authors.initials: T
authors.lastname: Endrawis
authors.affiliation: New Jersey Center for Science Technology and Mathematics, Kean University, Union, NJ 07083, USA. Electronic address: bowersau@kean.edu.
authors.forename: Autumn
authors.initials: A
authors.lastname: Bowers
authors.affiliation: New Jersey Center for Science Technology and Mathematics, Kean University, Union, NJ 07083, USA. Electronic address: ysun@kean.edu.
authors.forename: Yazhou
authors.initials: Y
authors.lastname: Sun
mesh_terms: D044962:Data Compression / Q000379:methods*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D015894:Genome, Human; D018745:Genome, Plant; D006801:Humans; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
keywords: Biologist-friendly NGS data compressor; Data compression utility; FASTQ compression; FASTQ sequence data compression; Integer-mapped k-mer indexing