Optimal reference sequence selection for genome assembly using minimum description length principle.

ABSTRACT: : Reference assisted assembly requires the use of a reference sequence, as a model, to assist in the assembly of the novel genome. The standard method for identifying the best reference sequence for the assembly of a novel genome aims at counting the number of reads that align to the reference sequence, and then choosing the reference sequence which has the highest number of reads aligning to it. This article explores the use of minimum description length (MDL) principle and its two variants, the two-part MDL and Sophisticated MDL, in identifying the optimal reference sequence for genome assembly. The article compares the MDL based proposed scheme with the standard method coming to the conclusion that "counting the number of reads of the novel genome present in the reference sequence" is n

SUBMITTER: Wajid B 

PROVIDER: S-EPMC3608252 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature