SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Cox, Murray P ^a,b,c   Peterson, Daniel A ^a   Biggs, Patrick J ^a  

^a MASSEY UNIVERSITY   (New Zealand)

^b Allan Wilson Centre for Molecular Ecology & Evolution   (New Zealand)

^c The Bio Protection Research Centre   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATED SOFTWARES; DOWNSTREAM APPLICATIONS; FLOW CELLS; ILLUMINA; QUALITY ASSESSMENT; RNA SEQUENCING; SECOND GENERATION; SEQUENCE DATA;

MOLECULAR BIOLOGY; NUCLEIC ACIDS;

GENE ENCODING;

ARTICLE; COMPUTER PROGRAM; DNA SEQUENCE; INTERNET; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS;

BASE SEQUENCE; INTERNET; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 77957151956     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-485     Document Type: Article

References (10)

1. Metzker ML. Sequencing technologies - The next generation. Nat Rev Genet 2010, 11:31-46. 10.1038/nrg2626, 19997069.
2. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008, 36:e105. 10.1093/nar/gkn425, 2532726, 18660515.
3. Dolan PC, Denver DR. TileQC: A system for tile-based quality control of Solexa data. BMC Bioinformatics 2008, 9:250. 10.1186/1471-2105-9-250, 2443380, 18507856.
4. Hannon GJ. FASTX-Toolkit. 2010, http://hannonlab.cshl.edu/fastx_toolkit/
5. Martínez-Alcántara A, Ballesteros E, Feng C, Rojas M, Koshinsky H, Fofanov VY, Havlak P, Fofanov Y. PIQA: Pipeline for Illumina G1 genome analyzer data quality assessment. Bioinformatics 2009, 25:2438-2439. 10.1093/bioinformatics/btp429, 2735671, 19602525.
6. Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, Naef F. Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics 2008, 9:431. 10.1186/1471-2105-9-431, 2575221, 18851737.
7. R Development Core Team R: A Language and Environment for Statistical Computing. 2010, R Development Core Team., http://www.r-project.org/
8. Pavlidis P, Noble WS. Matrix2png: A utility for visualizing matrix data. Bioinformatics 2003, 19:295-296. 10.1093/bioinformatics/19.2.295, 12538257.
9. Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucl Acids Res 2010, 38:1767-1771. 10.1093/nar/gkp1137, 2847217, 20015970.
10. Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829. 10.1101/gr.074492.107, 2336801, 18349386.