title: SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing.
abstract: BACKGROUND
  Next-generation sequencers (NGSs) have become one of the main tools for current biology. To obtain useful insights from the NGS data, it is essential to control low-quality portions of the data affected by technical errors such as air bubbles in sequencing fluidics.
  
  
  RESULTS
  We develop a software SUGAR (subtile-based GUI-assisted refiner) which can handle ultra-high-throughput data with user-friendly graphical user interface (GUI) and interactive analysis capability. The SUGAR generates high-resolution quality heatmaps of the flowcell, enabling users to find possible signals of technical errors during the sequencing. The sequencing data generated from the error-affected regions of a flowcell can be selectively removed by automated analysis or GUI-assisted operations implemented in the SUGAR. The automated data-cleaning function based on sequence read quality (Phred) scores was applied to a public whole human genome sequencing data and we proved the overall mapping quality was improved.
  
  
  CONCLUSIONS
  The detailed data evaluation and cleaning enabled by SUGAR would reduce technical problems in sequence read mapping, improving subsequent variant analysis that require high-quality sequence data and mapping results. Therefore, the software will be especially useful to control the quality of variant calls to the low population cells, e.g., cancers, in a sample with technical errors of sequencing procedures.
authors.forename: Yukuto
authors.initials: Y
authors.lastname: Sato
authors.forename: Kaname
authors.initials: K
authors.lastname: Kojima
authors.forename: Naoki
authors.initials: N
authors.lastname: Nariai
authors.forename: Yumi
authors.initials: Y
authors.lastname: Yamaguchi-Kabata
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Kawai
authors.forename: Mamoru
authors.initials: M
authors.lastname: Takahashi
authors.forename: Takahiro
authors.initials: T
authors.lastname: Mimori
authors.affiliation: Department of Integrative Genomics, Tohoku Medial Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku Sendai, Miyagi, 980-8573, Japan. nagasaki@megabank.tohoku.ac.jp.
authors.forename: Masao
authors.initials: M
authors.lastname: Nagasaki
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017422:Sequence Analysis, DNA; D012984:Software; D013223:Statistics as Topic / Q000379:methods*; D014584:User-Computer Interface
references.citation: Biomed Res Int. 2013;2013:865181
references.pmid: 24319692
references.citation: Bioinformatics. 2009 Jul 15;25(14):1754-60
references.pmid: 19451168
references.citation: BMC Bioinformatics. 2013 Jan 31;14:33
references.pmid: 23363224
references.citation: Nat Methods. 2012 Mar 04;9(4):357-9
references.pmid: 22388286
references.citation: BMC Bioinformatics. 2008 May 28;9:250
references.pmid: 18507856
references.citation: Bioinformatics. 2009 Aug 15;25(16):2078-9
references.pmid: 19505943
references.citation: Genome Res. 1998 Mar;8(3):175-85
references.pmid: 9521921
references.citation: Nucleic Acids Res. 2010 Apr;38(6):1767-71
references.pmid: 20015970
references.citation: BMC Bioinformatics. 2010 Sep 27;11:485
references.pmid: 20875133