Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data

• DOI: 10.1093/bioinformatics/btt434
• Publication Date: 2013-07-31T00:34:28Z
• Authors: Wenjie Deng; Brandon S. Maust; Dylan H. Westfall; Lennie Chen; Hong Zhao; Brendan B. Larsen; Shyamala Iyer; Yi Liu; James I. Mullins
• Keywords: Indel; Pyrosequencing; Perl; INDEL Mutation; Sequence (biology)

Abstract Motivation: Pyrosequencing technology provides an important new approach to more extensively characterize diverse sequence populations and detect low frequency variants. However, the promise of this has been difficult realize, as careful correction sequencing errors is crucial distinguish rare variants (∼1%) in infected host with high sensitivity specificity. Results: We developed a approach, referred Indel Carryforward Correction (ICC), cluster sequences without substitutions locally correct only indel carryforward within clusters ensure that no are lost. ICC performs clustering order (i) homopolymer patterns only, (ii) (iii) requirement distance cutoff value. Overall, removed 93–95% found control datasets. On pyrosequencing data from PCR fragment derived 15 HIV-1 plasmid clones mixed at various frequencies 0.1%, achieved highest similar specificity compared other commonly used error variant calling algorithms. Availability implementation: Source code freely available for download http://indra.mullins.microbiol.washington.edu/ICC. It implemented Perl supported on Linux, Mac OS X MS Windows. Contact: [e-mail] Supplementary information: Bioinformatics online.