Introduction

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

Publications

  1. Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data.
    Cite this
    Deng W, Maust BS, Westfall DH, Chen L, Zhao H, Larsen BB, Iyer S, Liu Y, Mullins JI, 2013-10-01 - Bioinformatics (Oxford, England)

Credits

  1. Wenjie Deng
    Developer

    Department of Microbiology, University of Washington School of Medicine, United States of America

  2. Brandon S Maust
    Developer

  3. Dylan H Westfall
    Developer

  4. Lennie Chen
    Developer

  5. Hong Zhao
    Developer

  6. Brendan B Larsen
    Developer

  7. Shyamala Iyer
    Developer

  8. Yi Liu
    Developer

  9. James I Mullins
    Investigator

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Summary
AccessionBT001190
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByJames I Mullins