Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly.

ABSTRACT:

Motivation

Eugene Myers in his string graph paper suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also encodes every valid assembly of reads, such a graph, provided that it can be constructed correctly, is in fact a lossless representation of reads. In principle, every analysis based on whole-genome shotgun sequencing (WGS) data, such as SNP and insertion/deletion (INDEL) calling, can also be achieved with unitigs.

Results

To explore the feasibility of using de novo assembly in the context of resequencing, we developed a de novo assembler, fermi, that assembles Illumina short reads into unitigs while preserving most of information of the input reads. SNPs and INDELs can be called by mapping the uniti

SUBMITTER: Li H 

PROVIDER: S-EPMC3389770 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature