SUGAR: Graphical user interface-based data refiner for high-throughput DNA sequencing

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Sato, Yukuto ^a   Kojima, Kaname ^a   Nariai, Naoki ^a   Yamaguchi Kabata, Yumi ^a   Kawai, Yosuke ^a   Takahashi, Mamoru ^a   Mimori, Takahiro ^a   Nagasaki, Masao ^a  

^a TOHOKU UNIVERSITY   (Japan)

Author keywords

Automated analysis; Data cleaning; Illumina HiSeq; MiSeq; NGS

Indexed keywords

ARTICLE; COMPUTER ANALYSIS; COMPUTER INTERFACE; COMPUTER PROGRAM; DNA SEQUENCE; GENE MAPPING; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; BIOLOGY; COMPUTER GRAPHICS; HUMAN; PROCEDURES; STATISTICS;

COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ANALYSIS, DNA; SOFTWARE; STATISTICS AS TOPIC; USER-COMPUTER INTERFACE;

EID: 84905984916     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-664     Document Type: Article

References (11)

1. Dolan PC, Denver DR. TileQC: a system for tile-based quality control of Solexa data. BMC Bioinformatics 2008, 9:250. doi:10.1186/1471-2105-9-250, 10.1186/1471-2105-9-250, 2443380, 18507856.
2. Cox MP, Peterson DA, Biggs PJ. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 2010, 11:485. doi:10.1186/1471-2105-11-485, 10.1186/1471-2105-11-485, 2956736, 20875133.
3. Yang X, Liu D, Liu F, Wu J, Zou J, Xiao X, Zhao F, Zhu B. HTQC: a fast quality control toolkit for Illumina sequencing data. BMC Bioinformatics 2013, 14:33. doi:10.1186/1471-2105-14-33, 10.1186/1471-2105-14-33, 3571943, 23363224.
4. Li B, Zhan X, Wing MK, Anderson P, Kang HM, Abecasis GR. QPLOT: a quality assessment tool for next generation sequencing data. Biomed Res Int 2013, 2013:865181. doi:10.1155/2013/865181, 3844194, 24319692.
5. FastQC. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
6. Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 2010, 38(6):1767-1771. doi:10.1093/nar/gkp1137, 10.1093/nar/gkp1137, 2847217, 20015970.
7. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G. Durbin R; 1000 genome project data processing subgroup. the sequence alignment/map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. doi:10.1093/bioinformatics/btp352, 10.1093/bioinformatics/btp352, 2723002, 19505943.
8. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. accuracy assessment. Genome Res 1998, 8(3):175-185. doi:10.1101/gr.8.3.175, 10.1101/gr.8.3.175, 9521921.
9. Sheikh MA, Erlich Y. Base-calling for bioinformaticians. Bioinformatics for High Throughput Sequencing 2012, 67-84. New York, USA: Springer, Rodri´guez-Ezpeleta N, Hackenberg M, Aransay AM.
10. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. doi:10.1093/bioinformatics/btp324, 10.1093/bioinformatics/btp324, 2705234, 19451168.
11. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9(4):357-359. doi:10.1038/nmeth.1923, 10.1038/nmeth.1923, 3322381, 22388286.