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

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 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.

Results

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 err

SUBMITTER: Deng W 

PROVIDER: S-EPMC3777116 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature