This is the Linux app named MARAGAP whose latest release can be downloaded as Data-Maragap.rar. It can be run online in the free hosting provider OnWorks for workstations.
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DESCRIPTIONThis paper presents `MARAGAP', a 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 those insertions and a Bayesian estimation framework for SNPs.
This is an application that can also be fetched from https://sourceforge.net/projects/refasp/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.