MARAGAP: a modular approach to reference assisted genome assembly pipeline
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Copyright © 2015 Inderscience Enterprises Ltd. This paper presents MARAGAP, a modular approach to reference assisted genome assembly pipeline. MARAGAP uses the principle of Minimum Description Length to determine the optimal reference sequence for the assembly. The optimal reference sequence is used as a template to infer inversions, insertions, deletions and SNPs in the target genome. MARAGAP uses an algorithmic approach to detect and correct inversions and deletions, a De-Bruijn graph based approach to infer the insertions, an affine-match affine-gap local alignment tool to estimate the locations of insertions and a Bayesian estimation framework for detecting SNPs.
author list (cited authors)
Wajid, B., Serpedin, E., Nounou, M., & Nounou, H.