Quality filtering of Illumina index reads mitigates sample cross-talk

BMC Genomics

Volumn 17, Issue 1, 2016, Pages

  Wright, Erik Scott ^a   Vetsigian, Kalin Horen ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Illumina; Multiplexing; Sequencing; Sequencing errors

Indexed keywords

DNA;

AMYCOLATOPSIS; ANALYTICAL ERROR; ARTICLE; CORRELATION ANALYSIS; DNA EXTRACTION; MOLECULAR INTERACTION; POLYMERASE CHAIN REACTION; QUALITY CONTROL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STREPTOMYCES; HIGH THROUGHPUT SEQUENCING; PROCEDURES; STANDARDS;

HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; QUALITY CONTROL;

EID: 84994482389     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-3217-x     Document Type: Article

References (12)

1. Cox MP, Peterson DA, Biggs PJ, Solexa QA. At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics. 2010;11:485.
2. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Research. 2008;36:e105-5.
3. Schirmer M, Ijaz UZ, D'Amore R, Hall N, Sloan WT, Quince C. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Research. 2015;43:e37-7.
4. Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, et al. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Research. 2011;39:e90.
5. McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP, Callahan BJ. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Meth. Nature Publishing Group; 2016;:1-7.
6. Wright ES, Vetsigian KH. Inhibitory interactions promote frequent bistability among competing bacteria. Nat Commun. 2016;7:11274.
7. Kircher M, Sawyer S, Meyer M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Research. 2011;40:e3-e3.
8. Nelson MC, Morrison HG, Benjamino J, Grim SL, Graf J. Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys. Heimesaat MM, editor. PLoS ONE. 2014;9:e94249.
9. D'Amore R, Ijaz UZ, Schirmer M, Kenny JG, Gregory R, Darby AC, et al. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genomics. 2016;17:55.
10. Leinonen R, Sugawara H, Shumway M, on behalf of the International Nucleotide Sequence Database Collaboration. The Sequence Read Archive. Nucleic Acids Research. 2010;39:D19-D21.
11. Wright ES. Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R. R Journal. 2016;8:352-9.
12. R Core Team. R: A language and environment for statistical Computing. Vienna: R Foundation for Statistical Computing; 2016. URL https://www.R-project.org/.