RT Journal Article
SR Electronic
T1 ProbAlign: a re-alignment method for long sequencing reads
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 008698
DO 10.1101/008698
A1 Feng Zeng
A1 Rui Jiang
A1 Guoli Ji
A1 Ting Chen
YR 2014
UL http://biorxiv.org/content/early/2014/09/02/008698.abstract
AB The incorrect alignments are a severe problem in variant calling, and remain as a challenge computational issue in Bioinformatics field. Although there have been some methods utilizing the re-alignment approach to tackle the misalignments, a standalone re-alignment tool for long sequencing reads is lacking. Hence, we present a standalone tool to correct the misalignments, called ProbAlign. It can be integrated into the pipelines of not only variant calling but also other genomic applications. We demonstrate the use of re-alignment in two diverse and important genomics fields: variant calling and viral quasispecies reconstruction. First, variant calling results in the Pacific Biosciences SMRT re-sequencing data of NA12878 show that false positives can be reduced by 43.5%, and true positives can be increased by 24.8% averagely, after re-alignment. Second, results in reconstructing a 5-virus-mix show that the viral population can be completely unraveled, and also the estimation of quasispecies frequencies has been improved, after re-alignment. ProbAlign is freely available in the PyroTools toolkit (https://github.com/homopolymer/PyroTools).